The doctrine of separation from "the unclean thing" is neglected today by professing Christians, but it is still here in God’s Word. The context indicates that Paul is warning against Christians being "unequally yoked together with unbelievers" and urging us to "cleanse ourselves from all filthiness of the flesh and spirit, perfecting holiness in the fear of God" (2 Corinthians 6:14; 7:1).
Such separation does not mean having no contact at all with unbelievers, "for then must ye needs go out of the world" (1 Corinthians 5:10), whereas Jesus commanded, "Go ye into all the world, and preach the gospel to every creature" (Mark 16:15). He also prayed to the Father, "not that thou shouldest take them out of the world, but that thou shouldest keep them from the evil" (John 17:15).
He does demand, however, that we are not to compromise with unbelief or with the unclean thing. We are "born again" into the family of God through simple faith in the person and saving work of Christ; but the full manifestation and fellowship of our relation with the heavenly Father as His spiritual sons and daughters is evidently, in this passage, conditioned on the vital principle of separation from all unbelief and filthiness of the flesh, with Jesus as our example (Hebrews 7:26).
We are specially warned to "turn away" from those who, "having a form of godliness," attempt to accommodate the naturalistic viewpoint of modern scientism within the Scriptures, thus "denying the power thereof" (2 Timothy 3:5). "Be ye separate, saith the Lord." HMM