Best way is with sprintf:

$u = sprintf "%06d", $u;
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If you want to use a substitution, you could do:

$u =~ s/(\d+)/"0"x(6-length($1)).$1/e; if length($u) < 6;
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Update: To correct your attempt:

if($u=~/^\d{4}$/){$u=~s/\d\d\d\d/00$u/;}
if($u=~/^\d{5}$/){$u=~s/\d\d\d\d\d/0$u/;}
# but better written as:
#  $u = "00$u" if $u =~ /^\d{4}$/;
#  $u = "00$u" if length($u) == 4;  # if you know it's digits
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