After trying the pro version of Recap and then speaking with Autodesk support, it appears that Recap cannot align unstructured point clouds on their own...rather, there needs to be at least one structured scan in the project. I'm not a software engineer, but it puzzles me why unstructured data could automatically (or with manual assistance) be aligned to structured data but not to other unstructured point clouds. I'd love to see this capability added.
Our current workflow is for scanning trees and surrounding exterior natural environments for treehouse designers & builders, bringing a level of accuracy far beyond their typical process and allowing them to design confidently in CAD. We started with a combination of 123D Catch (for proper alignment and scaling) and Agisoft Photoscan (for very detailed point clouds and meshes that could process locally on a machine in a few hours). The resulting redundant data sets had to be aligned manually in 3ds max then output as an obj mesh file for SketchUp or DWG for Autocad/Revit. Results were spotty, and meshes were hard to deal with. We'd like to transition to only using point clouds in all Autodesk tools...Recap, Revit, & 3ds max. Currently I can get close with Recap photo if I have one scan for the entire site (though often we have more and need to align them)...I can manually create survey points with reference distances, but proper vertical orientation is still unattainable directly in Recap (but was easy in 123D Catch). We'd love to see a solid photogrammetry workflow possible in Recap!