$filename2 is a web address. The web server translates the web address into a unix filesystem filename, based on how you have the web server configured. http://my_site/ is the web address of the web server, the next part, /cgi-bin/, is probably your cgi root, which is set up in your web server configuration, and translates to some absolute base path, in your case it appears to be /var/apache/cgi-bin/. The rest, user/test.txt refers to a specific file on that server.

So the web server filename translation changes your address to /var/apache/cgi-bin/user/test.txt, which is exactly what $filename1 is.

So, after all that, the web server automatically does that translation, but perl assumes that you are giving a relative or absolute pathname that is of the form your operating system normally deals with, i.e. it doesnt do the translation that the web server does. If you're much into unix, think about why a command like rm $filename2 wont work right. perl assumes filenames just like the unix shell does.

The reasons for the web address translation are many, it allows virtual hosting, and it also keeps me from doing something like http://your_server/etc/passwd - which you probably dont want me doing.

You should probably read up on apache & web server conifguration in general.