$number = 1;
$number = "0".$number until length $number >= 3;
print $number,"\n";

I'm sure merlyn just wanted you to know that although this works as expected, there are better alternatives. To many, "Matt Wright" is a synonym for "clumsy code that does however do what it's supposed to do" (not to be taken literally: merlyn didn't ask if you went to school with clumsy code :)).

Your approach is directly instructing Perl to do what you want it to do. If you feel comfortable with that, you should do it that way. But often there is some efficiency in both coding and run time to be gained when you use Perl's core functions. In this case, it'd be $number = sprintf '%03d', $number;, which is approximately 2.5 times as fast.

Learn about sprintf. It can be very confusing at first, but the %-notation is easy to get used to.

U28geW91IGNhbiBhbGwgcm90MTMgY
W5kIHBhY2soKS4gQnV0IGRvIHlvdS
ByZWNvZ25pc2UgQmFzZTY0IHdoZW4
geW91IHNlZSBpdD8gIC0tIEp1ZXJk