I have to do a laser scan on a building, located in a small city. There are some issues that I have come accross such as how to properly capture lidar data on a building where two of the sides are shared (there might be a minor opening) with other buildings and another side covered by trees. I am thinking of filling the holes in the 3d model with some type of color to show data could not be collected. Let me know what y'all think about that. scanning the other sides of the buildings, should I scan with the drone flight up to get all the data points to make sure I am not missing things, there are other buildings located pretty close, as this is in a city type environment.

Any tips or guidance would be appreciated.

When you say the buildings are close, are we talking footpath, lane or road between them? If the later and you can get reasonable GPS then you should be ok if you are using RTK.  If you are talking footpath, obviously it is a different matter.