A commom method I know to increase the contrast between two similar looking material in the SEM is to treat the sample in a low pressure plasma chamber, e.g. with oxygen as process gas.
As the different materials usually react diffently they are often easier to distiguish afterwards.
The morphology of the sample (as well as the chemistry) can of course be changed dramatically due to the plasma, but if you are only interested in an inproved contrast it may work.
1)Coat the sample with gold (not carbon) because it gives much better contrast.
2)If the SEM has the option, activate the "charge neutralizer" which improves the overal quality of the sample image, and then you can fine-tune the contrast much easier.
3)Use thiner ring in the WEHNELT cap, so as to reduce the distance between the top of the whenlet cup and the peak of the "V" shaped filament, which gives brighter contrast (maybe consult technician for this one).
4)If the SEM has the option, you can replace the tungsten filament with LaB6, which gives better contrast,
5)Try using an image analysis software to enhance the contrast of the image via post-processing. I used ImageJ and the "enhance contrast" option and I think it works well with nanofibers.
Try the OTO-Osmium-OTO technique for SEM processing. This will increase conductivity and perhaps contrast if more osmium is present. Also if you fix with tannic acid (and aldehydes) , you can get more uranyl acetate also, although en-bloc staining is not usually done with SEM processing. Good Luck.
Dear Apostolos: Thank you! Addditionally, it might be of interest if you would let us know your previous fixation procedures for the stuff you're processing...Then we might be able to comment a bit more specified.... Best regards and wishes, Wolfgang