How to generate pdf without any Type3 fonts?

Look at the end of the log-file of pdflatex. It will tell you which fonts are included and which are bitmap (pk) fonts.

A Type 3 font is not by default a bitmap font. It means only not a Type 1 one. This is the reason why a Type 3 font can also be a vector font. If there is no listed pk font in the log file, then you have such a type 3 font included. It may also be loaded by an image with \includegraphics

First off, most people use pdflatex nowadays. Change every image to pdf if possible replacing eps files by pdf using

     convert file.eps file.pdf

convert is found in the imagemagick package. Remove epsfig and use includegraphics instead.

Next run:

     pdffonts final_upload_document.pdf | less

to ensure that a type 3 font problem is actually the issue. If it isn't then the problem is most likely related to spaces in file names.

Next run:

     pdffonts each_image.pdf

to find any type 3 fonts on the individual pdf files to find which image is causing the problem. It could be an xfig or matlab problem, or a problem from another image generator.

If the contained pdfs don't create the issue, then it is most likely an include such as blackboard fonts that is causing the problem inside the source latex file.

Using the above method I found in particular that xfig in addition to matlab can cause the same artefacts if you are using export to latex+pdf part.

When you find the pdf + latex file you can run:

  xfig -specialtext -latexfonts -startlatexFont default

to start up xfig with the right settings. You also might find as in my case that the xfig image was generated some years ago that was to go into the paper, and that it now doesn't even open in newer versions of xfig giving a sigsegv fault. In this case your only option is to regenerate the image using the above xfig call.