Annette
Well only (easiest) way to remove layers is the purge command.This will remove layers that are not used or have nothing on them.
Now your 2nd problem, I'm guessing that there is somthing still left on those layers, maybe not that you can see ( I call them "GHOSTS"), erased blocks and what not. Solution to this would be to purge all and check off the boxed that says "Purge nested blocks" and then purge. That should be the answer to your problem.
John Kinney
Woodbrier Assoc.