There is a parameter in the VM Backend, which is this: "Show uncategorised child products in search results and modules?".
I guess you had to enable that. Furthermore, in the normal conditions, the child products shouldn't have any category. Because they are not standalone products. But apparently you need to choose a "category" for difference purposes.
Anyway, what you need to do is applying some coding hacks to category PHP file
to check if the product is parent or child; if it is a child, hide it.
This is a 100% custom coding modification and unfortunately we don't provide free support or step-by-step instructions for custom coding modifications.
You may purchase premium support:
and let us take care this modification for you directly on your website though.
By the way, did you see these topics:
(i just found those topics through google.com, if you do some further investigation, i am sure you will find some other topics as well)