You can do it from the OS it self...
From Maemo You have to install xterm... (If you dont have it install look at the HOW TO sticky)

Open xterm in xterm gainroot access (same as above)

now once in root do the following

cd /usr/share/applications/hildon
once in there look for the file name you are trying to delete by typeing ls in xterm(They are all going to end with .desktop) for example nmap.desktop
once you see the file delete the file with rm for example:
rm nmap.desktop
or
rm /usr/share/applications/hildon/nmap.desktop

You are done.

Good Luck