I installed Matlab 2017b, and found the script will remove some colored areas. For example,

Code:

contourf(peaks(100));saveas(gcf,'figure.eps','epsc')
epsclean('figure.eps','figure_clean.eps','GroupSoft',true,'combineAreas',true,'removeboxes',true)

Generates the following (I converted from eps to pdf for this preview):

figure_clean.pdf

figure.pdf

Do you have any idea? Thank you for making this tool, regardless!