Errors generated after Importing geomentry
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The clearance is present if I open the .stp model on any other cad software but its intersecting in hyperworks.
What happens if you modify the cleanup tolerance before import?
Before you click the final 'Import' button - go into the Topology area where you can set 'Cleanup Tolerance' to 'Manual' and enter a value - say, 1.e-6.
(You can also get there from File > Preferences > HyperMesh (Geometry) > Import Options - then go into STEP > Topology)
Does that make any difference?
Does it make any difference if you set the tolerance (click on the three-bar/hamburger icon) to a lower value - 1.e-5 or 1.e-6 then do the checks?