Hi Dagon,
Yes, it is possible to measure the volume and/or area of just a portion of the map in PhotoScan.
Open your orthomosaic or DEM. Then click on the DRAW POLYGON icon in the main (top) toolbar (it has the shape of a pentagon). Next, digitise around the object you want to measure. Double click to close the polygon. Then right click on the digitised line and choose MEASURE. This will then show you the volume and area as well as a profile of the digitised line.
Alternatively, you could also use CloudCompare (
www.cloudcompare.org which is free and open source to compute the volume of a certain region. This is how you would do it:
http://www.cloudcompare.org/doc/wiki/index.php?title=2.5D_VolumeBtw, CloudCompare might me useful to do some other analysis for your studies.
Sounds like some really interesting work you are doing in Peru (love that country).
DroneDeploy is quite expensive (if you use it frequently) and does not really give you much control over the photogrammetric processing. You are much better off using Agisoft Photoscan Pro instead; the educational license is quite cheap.
In case you are using one of the (newer) DJI drones such as the Phantom 4/Phantom 4 Pro or Phantom 3 Advanced, I highly recommend to use either MapPilot or DJI GS Pro to plan your aerial surveys (both only run on iOS devices though). It makes image acquisition really easy.
All the best for your work.
Regards
SAV