I agree with thelenm that your code seems to work just fine. I'm trying to figure out what you think it is doing wrong.

Input File
--------------------------
this is a test [[ this is a test ]]
this is also a test [[ this is also a test ]]

Output
--------------------------
this is a test
this is also a test

Code
--------------------------
#!/usr/bin/perl -w
use strict;

open(FILE, "<test.txt") || die "Error: $!";

while(<FILE>) {
   $_ =~ s/\[\[[^\]]*\]s*\]/ /msg;
   print;
}

close(FILE);
[download]

Seems to be working to me! -Eric