Separate
as it is used in this verse, means,
To set off by boundary, divide, sever.
This does not mean that we as Christians are required to set up boundary lines on the land and live entirely separate from the world.  Nor are verses like, "Wherefore come
out from among them,  and be ye separate...", to be confused with the frightening and unBiblical teachings of  'Christian' Separatists (who believe in a superior white race,
the insane rantings of Adolf  Hitler, and many other strange and ungodly things.)
We must look at each verse together with the rest.  God also tells us to be "in the
world, but not of  it"; to be, 'the salt of the earth", to be, "the light of the world",
to, "let your light so shine before men that they might see your good works",
and that we should, "go ye therefore and teach all nations".  God also requires
that we separate ourselves from immorality. 
We know that we are
not to be, "unequally yoked".
  We also know from 1 Cor 15:33, that
"evil communications corrupt good manners".  God also tells us
that we are to be separate from those who call themselves
Christians but are living in fornication or other sin 
(1 Cor 5:9).  Being wise in how we interpret the
scripture on "being separated", will
help us to be wise in our actions,
loyalties, affections,
and relationships.
Wherefore come out from among them,
and be ye separate, saith the Lord;
and touch not the unclean thing;
and I will receive you,
and I will be a Father unto you,
and ye shall be my sons and daughters,
saith the Lord Almighty.

2 Corinthians 6:17-18
More verses on being, "separate", or,
"in the world but not of it".
..
Mt 5:13-16
Mt 28-18-20
John 15-19

2 Cor 6:14-18
2 Cor 7:1
Eph 5:11
Col 4:5-6
1 Th 3:6
1 Th 4:3-5

Pr 4:14
Pr 24:1
Pr 28:7
Can you think of any examples of how not being separate from, or,"being unequally yoked together with" unbelievers or Christians who are living in fornication or other sin, could cause us to stumble and fall in our own Christian walk?