To perform a 3D analysis on an STL model, it is essential that the model is watertight before it is imported.
A watertight model is defined as:
Every triangle edge in the STL has exactly two neighbors. This implies that there are no holes or non-manifold edges.
Every node in the triangle is connected to only one "fan" of triangles around it. That is, for a given node, every triangle that shares that node must be accessible from any other triangle that shares the same node by moving across triangle edges. This is a further condition on the domain being a proper manifold.
There are no geometric overlaps or intersections in the model. This condition is independent of definition (1) above. An STL may be properly manifold but may still have overlaps and/or intersections due to triangles intersecting or overlapping with each other geometrically.
There are no geometric errors that produce unrealistically thin areas. This is essentially similar to an overlap, but may not be severe enough to be picked up as an overlap.