This solution works only for the Pro plugin version.
To make FiboSearch look only for products in certain categories, go to WooCommerce -> FiboSearch and choose the “Search config” tab. At the bottom of the config page, you’ll see the following section:
Set Filtering mode to “Include” and then set Filters to the categories you want to include in search. You can also narrow down the search to products with given tags.
Save you changes and rebuild the index. From now on, FiboSearch will search only for products in selected categories.