I feel dirty just executing command line commands in my perl script and it doesn't feel very professional

If you do it right, it's fine* - but backticks are usually not the "right" way to do it: Calling External Commands More Safely

In this case, see jo37's and my responses to PERL to AWS.

* Update: To be a little more specific: I personally think it's fine in the case of aws and other complex tools like that, and if you're not doing it in a tight loop where performance is important. For stuff like grep, cat, awk, etc., of course one shouldn't call external commands - afoken made a nice list in this node.