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Working with .stl files

I am working on a project where I am trying to combine two scans of a broken weld. I plan on using the combine weld in Abaqus to run tests on it so it needs to be watertight.

I took two pieces of metal and welded them together and then broke the weld. I then scanned the two separate pieces, the scans are currently in .stl format. Now I am trying to recombine the scans to recreate the weld. I just need the edge of the weld to line up. I haven't been able to find a program yet that will connect the two jagged weld edges.
 

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