One of the first things you usually want to consider, when looking a task to be done, is "what part of it can I automate?" With Perl, that often means looking for a module - and when you want to walk directories, File::Find should be the first thing that comes to mind.

There are also a number of problems in your script - trying to pass a filehandle (instead of a filename) as an argument to the script, lots of temporary variables, invoking 'system' unnecessarily and failing to check its return - as a number of other people here have pointed out. I'd usually correct those and explain how to do them better, but this isn't just a case of a poorly-written function or two - your approach is the largest problem. I'm just going to take the lazy way out and provide the solution, while hoping that you'll consider those problems from a new perspective.

Since I don't have your data set, and since much of your code is redundant and difficult to read, I'm going to take a few liberties and guess at what you're trying to do in places. You're probably going to need to correct a few things.

#!/usr/bin/perl -w
use strict;
use File::Find;

### User-modifiable variables ###
my $reg = 'AZT,IOP,AERTC';
my $week = 'W36';
### User-modifiable variables ###

# Get the dirlist for File::Find
my @dirs = glob "semaine_$week/Regulation_{$reg}";

# The 'find' subroutine comes from 'File::Find'
find(\&process, @dirs);

my %seen;
sub process {
    # Skip if we've already processed the file in this directory
    next if $seen{$File::Find::dir};
    # Skip unless the file matches the spec
    next unless /^slot_list\w*.\d\d\.01\.\w+\.out$/;

    # We've found the file that we want; now, we'll process it
    open Out, ">results.csv" or die "results.csv: $!\n";
    open Fh, $_ or die "$_: $!\n";
    while (my $line = <Fh>){
        chomp $line;
        my ($key, $val) = split /;/, $line;
        print Out "$key;$val\n";
    }
    close Fh;
    close Out;
    # Mark directory as 'processed'
    $seen{$File::Find::dir}++;
}
[download]

Update: Corrected the regex. I'd already fixed it in the script, but still had the old copy in the buffer...

-- 
Human history becomes more and more a race between education and catastrophe. -- HG Wells