Hello Robbih and welcome to the Monastery. First, KUDOS for getting the standAloneBlast to run ;). I gave up on it a long time ago.

I wonder if the files that are generated by the BLAST factory are temporary files. In that case you may simply add $fac->cleanup;. But before that you might need to register the files for deletion. You've not indicated whether you explored this option but it is mentioned in the same link you quoted. Otherwise you might consider explicitly deleting the files yourself by using the Perl unlink function.

Asking BioPerl related questions maybe a bit tricky since not all the Monks are into bioinformatics for that me and BioLion have written Perl and Bioinformatics which you might find useful when interacting with monks in the Monastery.