"However, the script is not finding the files."
You may not be telling rm to look in the right directories. You might have to cd to the right directory before you issue rm. You may need the -R option on the rm command. See man rm.
If your search criteria is too complicated for a simple * you could some variation of this command:
find /home/user/* -iname "*.~" -exec rm {} \;
You can find an explanation of what this means here:
http://www.linuxquestions.org/questi...hreadid=167901
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Steve Stites