3D scanning is typically not good for replicating mechanical parts. You’re far better off re-modelling the part in a good MCAD package and taking dimensions off the original part with calipers.
The only exception might be in the case of an object with a lot of compound curves and spline surfaces.
As far as STL files go, they are not the easiest files to edit and manipulate because they typically are composed of many thousands of individual polygons - typically triangular facets. There are tools such as meshmixer than can help. You’d be better off starting with a file that contains pure parametric geometry to be able to easily make changes. An industry standard format like STEP is good, but every MCAD program typically has their own.
Do you have any 3D MCAD tools or experience? Also, how big is the part you are looking to modify and recreate?