Thank a lot wise Monks.
I finally figured it out before seeing your replies:

my $logname = `logname`; chomp($logname);
my @output = `ps -ef | grep $logname`;

foreach(@output) {
  chomp;
  next if /\~$/ || !$_;
  my $file = $_;
  if ($file =~ /^.*\/export\/home\/$logname\/(.*)\/bin\/.*?/) {
    print "$1\n";
  }
}
[download]

Displays what I want:
folder1
folder2
folder3

The soluce was indeed in the array instead of the string.