Your system statement passes the string rm index.html?C=S;O=D to the unix shell. Since the semicolon has special meaning to the shell (it is a command separator), the shell breaks your string up into 2 commands:

rm index.html?C=S
O=D
[download]

Since you do not have a file named "index.html?C=S", you get the "No such file or directory" message.

Try to replace your system with unlink:

unlink $filename or die $!;
[download]

If that doesn't work, you may have to resort to some type of escaping heroics using backslashes or quotes.