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Should I de-feature CAD geometry prior to FEA?

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The answer is yes and no. Do not blanket strip out all fillet radii because in doing so you may be introducing a stress singularity if you create a sharp corner in an area of interest. 

On the other hand, chamfers and rounded edges on the end of plates usually don't affect the FEA results so it's usually better to de-feature these.

Small holes can also be removed provided they are not in the area of interest.

If in doubt, don't de-feature since the geometry can be de-featured with the FEA software program.

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