Maybe the PDF export options "AllowRasterization"->False or ImageResolution->300 (for example) would help.
According to the reference page for PDF export,
"Mathematica does not rasterize fonts or 2D vector graphics when exporting to PDF."
http://reference.wolfram.com/mathematica/ref/format/PDF.html, under Import and Export.
Are you drawing the flow chart with the Drawing Tools palette? or with primitives like Line and Rectangle?
re: "draw a flow chart on a surface":
If you have the flowchart in a graphic and want to place it over a non-flat surface, Texture might help.
As Bill Simpson pointed out, a modest-sized notebook example would help us a lot.