The extract function seperated each face?

Select all the faces at once you wish to seperate(if they are ajoined its the best), when you seperate them, select the object, move it a few units away to work on it in the open, keeping the verts that alight it with the other object alone. When your done set its position to 0,0,0 (local) and combine it with your other object. merge verts and you should be set.

If it doesnt work it might help if you put up a screenshot or a render.(screen with wireframe on shaded would be best)

Ill be in the topic for a while to reply.(lurking)