There's More Than One Way To Do It... this one is cross-platform:

use warnings;
use strict;
use File::Spec::Functions qw/splitdir catdir/;

while (my $line = <DATA>) {
    chomp $line;
    my $out = do { local $.=0;
        catdir grep {$.++;1../^\d+\.\d+$/} splitdir($line) };
    print $out, "\n";
}

__DATA__
/fd/gfree/tere/frf4545/geerg/fds/0.1/fsdf/dsakdsa/
/fd/gfree/tere/frf4545/geerg/dfds/5.9/fdsf/fdsfd/
/fd/gfree/tere/frf4545/geerg/dsad/02.44/fdsf/fdsf/
[download]

Output:

/fd/gfree/tere/frf4545/geerg/fds/0.1
/fd/gfree/tere/frf4545/geerg/dfds/5.9
/fd/gfree/tere/frf4545/geerg/dsad/02.44
[download]

Updates 1 and 2: Updated the code above to better limit the scope of the local $., and the map {...?$_:()} is better written as a grep.