save transparency scatter plot .eps

I am desperatily trying to save a figure, that has scatter plots as subfigures in .eps for a publication. To avoid overplotting I used transparency in the scatter plots (alpha = 0.01).

When I am saving the figure via the print('-depsc2', ...) command the transparency is not saved one basically sees nothing. When I am saving the figure manually via 'File'->'Save As...' the resolution is the screen resolution, which is unacceptable here, too.

Do you have a way out? Thanks a lot!