IEEE always requires authors to embed all fonts for the final pdf submission. After some googling, the commands that works for me under Ubuntu are
dvips -Pdownload35 -t letter -G0 -o paper.ps paper.dvi
ps2pdf -dMaxSubsetPct=100 -dCompatibilityLevel=1.2 -dSubsetFonts=true -dEmbedAllFonts=true paper.ps paper.pdf
If you have eps figures that are generated from matlab, most likely some fonts in the figures are still not embedded. You can run the following command if so
ps2pdf13 -dPDFSETTINGS=/prepress paper.pdf paper_final.pdf
If you need Acrobat version 5 or above. Try
ps2pdf14 -dPDFSETTINGS=/prepress paper.pdf paper_final.pdf
instead.