In deformable object manipulation, we often want to interact with specific segments of an object that are only defined in non-deformed models of the object. We thus require a system that can recognize and locate these segments in sensor data of deformed real world objects. This is normally done using deformable object registration, which is problem specific and complex to tune. Recent methods utilize neural occupancy functions to improve deformable object registration by registering to an object reconstruction. Going one step further, we propose a system that in addition to reconstruction learns segmentation of the reconstructed object. As the resulting output already contains the information about the segments, we can skip the registration process. Tested on a variety of deformable objects in simulation and the real world, we demonstrate that our method learns to robustly find these segments. We also introduce a simple sampling algorithm to generate better training data for occupancy learning.