what tech might work for high resolution (100 micron) 2.5d scan in x,y, and z?
time of flight sensor would have a larger spot size afaik and may not work for that reason
This might not be a helpful answer, but back in school we asked the med folks put things we wanted to copy through the CT scanner 
I think Magics RP was the software we used to create STLs from point clouds, but it’s been a while.
How small is very small? Inch?
You could try using a confocal microscope to capture several xy-plane slices of your object across the z-axis. Then, use a free application like 3D Slicer to fill in each slice and render a 3D object at the end.