Are you closing the excel application properly when done? Have a search with google on that:
http://www.google.nl#q=c%23+excel+dispose+properly[
^]
Another thing you might look at is the temp folder. Are you storing some files there temporarily? Then remove those when done.
Also, be aware that excel isn't meant to run as server app so if there is an alternative you should use that instead.
Good luck!