Solid models represented by Brep (not Mesh) may have lots of details, small features. I wish to know if there are rules or algorithms that will remove all those details and retain just the overall/principle shape. It is a defeaturing issue, but not for FEM, but relates only to geometry.
There are smoothing algorithms which will smoothen curvy areas faster, therefore removing small details. The ones I know are based on discrete mean curvature flow of Willmore flow. Mean curvature flow reduces area, hence bumps, but also global area, so it should be mitigated with either a dilation factor (to preserve global volume) or feature preserving terms. See Hildebrandt & Polthier and subsequent works.
Feature recognition and defeaturing of CAD models is still an active research area. Most CAD software provides some automated and manual methods for identifying "features" and suppressing them. In most cases they require the model to have been built in the CAD tool's environment and use parametric modeling to identify features. There is a technology that uses the "medial object". Also known as the "skeleton" of the CAD model. It is a dimensionally reduced version of the CAD model that can provide information about the general characteristics of the geometry. It has been used for automatic defeaturing, mesh sizing, hex meshing and even animation applications. CADFix from Transendata in the UK has a commercial code that uses the medial object. I am sure there are a handful of others.
What is the format you are following? Write algorithm to extract boundary elements of the required shape and write in separate file according to your requirement which can be used for further processing.
This is simple you follow the native format of feature based modeling software or neutral format like STEP, IGES.
Avoid using format like STL/3DXML/U3D/3DVRML as these are using mesh and computationally expensive to extract B-rep entities. These are very good for visualization purposes.