Sure you just need to use a regular expression. Open each file and loop over each line like this:

while( my $line = <IN> ) { 
    chomp($line); 
    $line =~ s/\[//g;   # Remove ['s  
    $line =~ s/\]//g;   # Remove ]'s 

    # Either print out to STDOUT here or 
    # write to another file 
}
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