Better ways to filter out features in scenProc that are overlapping with others or that are close together have been requested for a while already and I have now implemented a new step called FilterFeatures that adds these possibilities.
With this new step you can for example remove all point features of trees that are close to a round or remove buildings that have bounding boxes that are overlapping with other buildings. Please check the manual for the details and examples of how to use this new step.
Some of this filtering could be done before by using the AddAttributeIfInside step, for example to add an extra attribute when a feature was inside another feature and then filter them out based on this attribute. But the new step will make this kind of filtering a lot more efficient.