I have SEM image of cross section of multilayer thin film sample and need to represent the different color for different layer without losing its morphological information on the image. Is there any free software for doing such type of job ?
Tiff images can contain metadata, so you can try opening it with Gwyddion and play with the scales.
If your materials don't appear at different scaling levels, however, you probably will have to do the morphological evaluation first and then proceed with Photoshop, Photopaint or GIMP (the last one is free). Depending on where you publish that, you might have to declare that; e.g. ACS has a declaration form in its submission system for that.
Digital Surf is selling a version of Mountains (metrological topography software) that has a "SEM" version for 3D stereo reconstruction but also does colourization. Pretty nice results...but, it's not free.
If you're limited to free software, try GIMP and work as a digital graphics guy would : detour, select and use layers to colourize.
Or, if your sample allows it, you can use two or more detectors to generate different contrasts : use one detector image as the Red layer, another as the Green layer, etc and generate a colour image from your contrast texture (still using the GIMP).
Nowadays, for publishing manuscripts in high impact factor journals, SEM (Scanning Electron Microscope) images need to be false colored for enhancing visual illustration.
One can add colors to the SEM image using Adobe Photoshop CS3 or usual photoshop...