The purpose of this stage is to convert our Agisoft Photoscan mesh to something human-usable. In other words, the terrible poly-mess that Photoscan creates needs to be fixed in an external program - ZBrush can be used for this purpose as it has very easy to use automatic tools for our needs. Basics steps in this process are:
01. Import mesh and convert to Poly 3D
02. Clean the mesh - Photoscan, based on some errors, usually creates some additional floating objects/poligons around the main object. These might be totally invisible at times and need to be removed as they will be in the way in both retopologising and unwrapping.
03. Cap all of the holes - there might be holes in the object initially left from Photoscan or you might need to close the whole from the pedestal/turntable on which the object was placed while scanning.
04. Duplicate mesh - you need to keep your original ugly high-poly mesh until the end of the process so you can always bring back your details
05. Decimate the duplicate - in order for ZRemesher to work more easily you need to get a better, low-poligon mesh as a start.
Documentation: http://docs.pixologic.com/user-guide/zbrush-plugins/decimation-master/
06. Retopologise - for this purpose you can use ZRemesher, which is an automatic tool. Default settings produce fairly good results but sometimes you won't get what you need and some experimentation will be needed.
Documentation: http://docs.pixologic.com/user-guide/3d-modeling/topology/zremesher/
07. Project detail back and repeat Step 06 - often times, especially with more complex models, the first topology we get with ZRemesher has quite a few flaws, to the point that even the general shape of the object isn't correct. In such cases, you will need to repeat the process once more (sometimes a few times more). Unhide our original mesh and then Project its details on to the retopologised one while subdividing it in the meantime until you have identical details in both. Then repeat.
Documentation: http://docs.pixologic.com/user-guide/3d-modeling/topology/zremesher/transferring-detail/
08. Unwrap - when happy with the topology you can use UV Master to automatically unwrap our object. Always work on clone so you don't ruin your work. UV Master is automatic so if you do want some very specific seams placed you can export the model at this stage, unwrap in external software of choice and import it back afterward. Remember to work on the low-poly version!
09. Project details back - after unwrapping repeat Step 06.
10. Export - at this point it's wise to export both the High-Poly and Low-Poly objects of the new retopologised and unwrapped mesh. If you do this after texture creation you might experience object shift when exporting back into Photoscan and you won't be able to create your Diffuse Map.
Watch the video below for more graphical explanation of this process:
From here we can continue to the next stage where we will bake some textures in ZBrush.