The word 'Free' in the title of our denomination was selected by our founding fathers all those years ago to reflect this very point. Separated unto the Gospel, the little booklet published and distributed by our North American churches, [available online here] has the following to say about this point:
Many evangelicals have stayed in apostate churches. Others have separated but have not made any strong protest against the betrayal of the gospel by apostates and by the compromise of those evangelicals who have put denominational loyalty before obedience to the biblical command to separate. We view our freedom as liberty to stand resolutely for Christ, to defend the gospel, to oppose apostasy and compromise, and to urge God’s people to cease all fellowship with the unfruitful works of darkness. For us freedom is freedom to be holy, observing both personal and ecclesiastical separation unto the Lord.
Ecclesiastical Separation is expressly commanded in the Scriptures. There are five specific New Testament commands which relate to this matter:
1. We are to ‘mark’ those who teach error, cp. Romans 16:17. We are to take heed and observe what purports to be the truth. The word ‘mark’ has the sense of ‘scrutinising’. We are therefore required to examine that which comes along professing to be of God. We are not to gullible and just accept things at face value. We are warned: believe not every spirit, but try the spirits whether they are of God: because many false prophets are gone out into the world, 1 John 4:1. There are many who corrupt the Word of God, cf. 2 Corinthians 2:17. It is a wholly unscriptural position to adopt whereby we accept and believe everything that comes along professing to be of the Lord. We must mark out those who depart from the truth and cause divisions and offences contrary to what we have learned from the Word of God.
2. We are to ‘reprove’ those who teach error, cp. Ephesians 5:11. Silence is not an option in the face of false teaching and departure from the faith. When the unfruitful works of darkness have been observed we are not to remain silent less we create division. Truth is more important than false unity. There is an onus upon all who love the Lord Jesus to speak out in defence of His Truth and for His honour.
This is not a token expression of unhappiness. The word ‘reprove’ suggests strong rebukes with the intention of convincing someone of the wrong they are teaching or practicing. There must be the strongest refuting of error that is possible. Nothing less is agreeable to God’s Word.
It is only be rebuking the preachers of error that the truth will be safeguarded. The prophet of old was told to: cry aloud and spare not, lift up thy voice like a trumpet …, Isaiah 58:1. The true minister of Christ will speak out against error wherever it is found. He has a God given duty to do so, cf 1 Timothy 4:1-6.
3. We are to ‘reject’ those who teach error, cf. Titus 3:10. Instead of associating with them and seeking to bring them around to our way of thinking we are to reject them when there has been a repeated refusal to forsake false teaching or practice. We must reject those who persist in propagating error. Just as the physical body seeks to eradicate and reject a virus that is harming it, so the spiritual body must do likewise. These false teachers are not to be looked upon as belonging to the Church of Christ. They are to be denounced as the bringers in of damnable heresies, cf. 2 Peter 2:1.
4. We are to have 'no fellowship' with those who teach error, cf. 2 Corinthians 6:14-16. There can be no common ground between truth and error. It is impossible to jointly worship the Lord as is the case in numerous ecumenical services and functions, God is a Spirit: and they that worship him must worship him in spirit and in truth, John 4:24. Truth and error cannot worship God side by side. This is contrary to the plain teaching of these verses. There can be no fellowship, communion, concord, part or argument between those who are different in nature - clean and unclean. There was to be no yoking of clean and unclean animals together in Old Testament times. The same principle applies in New Testament times. This cannot happen because of the difference in principles, properties, personalities, profession, or policy.
There can be no voting for those who teach error. The word 'agreement’ in v16 is associated with voting, cf. Luke 23:51. Joseph of Arimathæa refused to support their assault on Christ. Evangelicals would do well to remember that when they vote for deacons, elders, ministers and moderators who reject the truth, 2 John 7-11.
5. We are to ‘separate’ from those who teach error, 2 Corinthians 6:17,18. The word ‘separate’ means to mark off by boundaries. We are required to mark off a boundary beyond which we will not cross. False teachers and their errors must be out of bounds to us. They are beyond the pale. We are not to be involved in denominations or alliances where false teachers are given recognition or encouragement. There is to be no co-operating with false teachers in any evangelistic or humanitarian venture.
From what/whom are we to separate? I believe this to be an important topic. After all the Bible warns against the sin of schism, cf. 1 Corinthians 1:10; 11:18;12:25. There is therefore legitimate scriptural separation and there is sinful schism. We may well ask: from what then are we to separate?
Generally speaking we should have no denominational links with those who reject the fundamentals of the faith, particularly those fundamentals which impact upon the person and work of Jesus Christ. We can highlight four areas:
1. We must separate from denominations which are Liberal and Modernistic in their theology. By 'Liberalism' we mean that spirit of criticism of all theological claims. By 'Modernism' we mean that preference for the new over the old. It is that critical thinking of the higher critic which begins with a repudiating of the doctrine of divine revelation and inspiration of the Bible. It ultimately leads on to the denial of the fundamental doctrines of divine revelation. In the place of the gospel of peace liberalism/modernism preaches the social gospel of the Fatherhood of God and the Brotherhood of man.
God’s command is crystal clear: Proverbs 19:27 Cease, My son to hear the instruction that causeth thee to err from the words of knowledge.
2. We must separate from denominations which are ecumenical in their practice. The 'One World Church' is the subtle ploy of the devil. The World Council of Churches [WCC] has long progressed from seeking union with Rome to desiring the union of all religions.
Ecumenism is preparing the way for the kingdom of antichrist. It is the habitation of devils, and the hold of every foul spirit, and a cage of every unclean and hateful bird, Revelation 18:2. Romanism is not Christian. It is paganism.
3. We must separate from denominations which are Neo-evangelical in their ethos. This is the most subtle of the foes that face the church today. This was a title first coined in 1947 by a Boston minister to denote the views of evangelicals who repudiated ecclesiastical separation and practiced inclusivism.
 Neo-evangelicalism wishes to embrace modern scholarship. Particularly modern scientific scholarship, which is not dogmatic about what they describe as debatable Biblical questions such as: creation, the age of the earth, the universality of the flood etc.
 Neo-evangelicalism wishes to abandon the old contending spirit of the past. It wants dialogue about the faith instead of fighting the good fight. Therefore, they cooperate and fellowship with liberals and modernists in writing books, evangelistic crusades, humanitarian ventures. They host seminars for discussions with apostates instead of rebuking them as the Scriptures exhort.
 Neo-evangelicalism wishes to put a greater emphasis upon dealing with society's problems. They participate in ventures where issues such as social justice, racism, poverty, etc. are campaigned against. It is not that this was never done in the past by the Church of Jesus Christ. It was done, however, within the bounds of separation.
The best and the only way to deal with society's problems is by the preaching and embracing of the Gospel. Today's society is seeking to have it both ways - to have its sin without the consequences. That won't happen. Sin brings misery and sadly it is the most venerable that suffer the most. The answer to the ills of today is not a social gospel but the triumph of the gospel of saving grace.
4. We must separate from denominations which are charismatic in character. The charismatic movement is present in its own right in pentecostal churches and also has infiltrated mainline denominations. Three things define the beliefs of the Charismatic movement. Belief in:
 Restorationism. This is the belief that the supernatural gifts of the apostolic church are available for the church today.
 Continuing revelation. The belief that God speaks to His people, collectively and personally as He did in the N.T. Church. That the Holy Ghost gives new, authoritative, extra-Biblical revelations today, which are binding upon the people of God
 Ecumenism. They pursue unity on the basis of experience rather than revealed truth. David du Plesis [Mr Pentecost] insisted that to be truly charismatic you must be ecumenical and to be truly ecumenical you must be charismatic. It is easily seen that these three points pose a serious threat to the purity of the Gospel and the calling of the Church to contend for the faith.
The practice of Secondary separation. In the past the FPC practiced what is commonly known as 'secondary separation'. That is, we refused to have fellowship with professing evangelicals who associated with Liberals, Modernists, Ecumenists, Neo-evangelicals and charismatics.
These individuals may be saved themselves but they fail to practice ecclesiastical separation in their own lives and in their denominations. Therefore we must separate from them. This is the express teaching of the Word of God, 2 Thessalonians 3:6 Now we command you, brethren, in the name of our Lord Jesus Christ, that ye withdraw yourselves from every brother that walketh disorderly, and not after the tradition which he received of us.
The principle of this text applies to much more than ecclesiastical separation. It teaches us that we are not to keep on fellowshipping with those who profess to be the Lord's yet are walking contrary to the truth of the Gospel.
In conclusion we must remember that the mixing of truth and error is deadly. The Christian is to be discerning and obedient to Scripture in the command to be separate as to our ecclesiastical associations.