Since the holes are "hidden" internally, you'll need to change the STEP Import option "Extraction Method" to use "Edge" and not the default "Surface Extraction".
Here's the definition for Extraction Method,
|Extraction Method: Instructs FAB 3000 how to generate 2D geometries from 3D STEP.|
|Surface||Generate 2D boundaries using surfaces. FAB 3000 will create a new layer for each surface it encounters. Thus even a single layer STP file will have a minimum of 2 surfaces (Top / Bottom).|
|Edge||Generate 2D boundaries using Edges that interest a parallel plane.|