I recently found myself needing to excise all of the type 3 fonts from a TeX document. I believe that type 3 fonts are actually just embedded postscript, which is less than ideal for a nice PDF. Obviously, I would never intentionally include a type 3 font, so some other tool in my toolchain must have been adding them. Eventually, I figured out that they were sneaking in through some matplotlib graphs. I found a nice description of the problem. The solution I chose was to tell matplotlib to use TeX-compatible output:
This fixed my output: all of my graphs now have proper type 1 fonts. This particular solution had one interesting side effect: all of the labels in the graphs were interpreted by TeX. This meant that some characters had to be escaped and that I was able to use some nice TeX amenities in labels.