My process is a little complicated. I'll try to explain it.
I created a folder, in my drive, containing all isometric minecraft blocks, in any possible orientation and configuration (you can see almost the whole set here: Standard Texture Showcase
Each PNG is named with a three-letters code. For example, the classic ground block with grass on top is named GRS, the dirt block is named DRT, the stonebrick block is STB and so on.
An example of a row of this file is "GRS,GRS,DRT,DRT,STB,GRS".
The HTML page read this array and visualize the whole creation in isometric. Each layere can be visible or invisible pressing a button.
With the same information it shows also the top view, using thumbnails I created apart.
I then proceed to take a snapshot of each layer, then I page them all together to create the final PDF.