chdir "/home/main/sub/oldfiles";  # or wherever
open READ, "$file"    # open READ ">$file" is a typo, no?
    or die "Couldn't open $file to read: $!\n";
# ... Do stuff, ready to write
open WRITE1, "> ../newfiles/$file"
    or die "Couldn't open $file to write: $!\n";
# ..Whatever...
open WRITE2, ">../../cgi-bin/$file"
    or die "Couldn't open $file to write: $!\n";