Articles submitted to IEEE conferences will have to meet IEEE Xplore PDF requirements. Most conference websites give free access to the PDF eXpress tool that can generate compatible PDFs from several source formats and validate PDF submissions as well. However, if you want to save time and generate such PDFs on Linux, here are the commands to use:
rm -f *.blg *.aux *.log *.aux
latex paper.tex
rm -f paper.bbl
bibtex paper
latex paper.tex
latex paper.tex
dvips -Ppdf -tletter -G0 -D 600 -o paper.ps paper.dvi
ps2pdf14 -dEmbedAllFonts=true -dUseFlateCompression=true -dPDFSETTINGS=/prepress paper.ps
NOTE: The template that your worked with, might not be compatible by itself. Avoiding hyperref package, fixed annotation related issues that PDF eXpress was complaining about.
Use these commands to generate high quality PDF documents for publishing. Change the paper type in ‘dvips’ command to suit your specs.