Always use strictures (use strict; use warnings; - see The strictures, according to Seuss). Use meaningful variable names. In particular, never be tempted to use names like 'tempN'. $temp1 should be $currCat, $temp2 should be $currFile and temp3 could be $currMethod.

You use %myData and %mydata. They should probably be the same thing. Strictures would have alerted you immediately. Correcting that and using your sample data prints:

Functions
Alpha.dat
MNO
Methods
Beta.dat
ABC
[download]

See other replies for a better solution to your problem.