Normally, executables that are made for another OS aren't going to work on Linux. The "setup.exe" leads me to believe this is the situation. However, to answer your question (if this is indeed a linux application):
Open up a terminal, and change to the directory containing the file in question. Then:
chmod 777 filename.exe
And then execute it with:
./filename.exe
Where filename is of course the name of the file you want to execute. For software that's made to work for Linux (usually) check out either your distro's install CD's, your distro's FTP, and/or
www.freshmeat.net
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