Have the same issue importing a 2D PDF into MoI3D which becomes a vector outline drawing for eventual export as a 2D DXF. Too many extra lines which come in with the PDF probably because the original drawing was either drawn with too many layers or has blocks created in the original software than converted to PDF. Unfortunately they are all on one layer after importing so it is not a matter of turning off layers. In MoI3D I run a command called RemoveDuplicates or if I take it into AutoCAD I run a command called Overkill. There might be something for similar for Inkscape perhaps.
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