I am interesting in more information about the analysis of 3D maps generated from 2D maps and DTM (literature, which type of file can be analysed, software names).
I guess, you will not make a mistake if you start with the ESRI ArcGIS and ERDAS Imagine software suites. Their tutorials are quite good and they can show you some directions.
As your concern is regarding calculation of landscape metrics, I would recommend you to use Fragstats as it is designed specifically for this purpose. However, Fragstats cannot handle calculation of 3D metrics, nevertheless, I believe that you can easily create new formulas for respective indices by defining a Z variable and perhaps utilize them in ArcGIS ... Also please take a look at the article below.
BTW: As I am also very curious about this, I would highly appreciate if you could update me of any progress on this.
Thank you very much, Vladimir, Zaagane and Javier for your answers, I will test the software you advised.
Mahyar, thank you for your detail answer and for the literature reference which is really helpful. I will gladly keep you informed of my progress on the subject.
Basic calculations like slope, aspect, curvature, etc., can be done using GDAL as well - freeware, open-source. I highly recommend SAGA GIS as the best option though.