How did you detect this contamination and how does it influence to your work?

The main effects are the presence of persistent "chromatic" aberrations which are no possible to overcome by simply tuning the X-Y astimgmators. When dismounting the Wehlnet, the anode and the aperture, it is possible to observe a reduction/distortion of the (normally circular) cross section.

I think, the problem isn't in contamination of whole microscope. Probably, there is a contamination of aperture - just clean it with heating (read the manual) or replace. The Wehnelt and the anode can be contaminated too, but, obviously, it isn't hydrocarbon, just tungsten, evaporated from cathode. Clean them with a polish paste.

The most common cause of the nonremovable aberrations is EM fields. Check your microscopy room.

Good luck!      

Here we clean wehnelt & anode with polishing at every filament exchange (I think this is common practice) while apertures (at least "the one", which is mostly used) are exchanged one-per-year. It becomes significantly smaller due to HC baked on it! While at service stage, check the polepiece for any possible magnetic stuff! That should be it... TEM's have "bake-out" options (Jeol) or sort of plasma-cleaning (FEI), but this is mostly done to achieve sufficient vacuum less to remove contamination. I'm not aware of similar procedures on SEMs though...

We also use to clean the wehnelt & anode with polishing + ultrosound bath in acetone, rinsing in IPA and drying with high purity Nitrogen.

The "beake-out" and the plasma approaches sounds really interesting for the HC contamination. Are they applied only for the observation chamber or the column is also taken into account? Thanks!

Of course wehnelt and anode should be clean each time the filament is changed to remove the carbon contamination  (if there is tungsten evaporation you may have a vacuum problem in the gun). It's also very important to keep clean all the column by an annual cleaning (At least to change the diaphragm) because all the parts that are irradiated by the beam end up contaminating. A good way to check if the column is clean is to work at low voltage and check if the stigmators need to be strongly adjust or not. If the column is too much dirty probably stigma correction is impossible at low voltage. Unfortunately most of us cannot clean the column for ourselves and we must call a service engineer.

This contamination mainly comes from the pumping system if the SEM used pumps working with oil as diffusion pumps or rotary pumps do. This oil backstreaming can be reduced by using a nitrogen trap between the chamber and the last pump of the circuit or directly inside the chamber. Liquid nitrogen cooled EDS systems acte also like trap because they are the coldest part in the chamber !

I use plasma cleaner to remove contamination but only to clean samples because I put it in the airlock chamber of my SEM.  probably a long plasma cleaning of the chamber can clean some parts but not the insides of the column (distance between plasma and the part to be cleaned is important).

One of my SEM has Low Vacuum mode. Instead of air from the room I have connected nitrogen at the entry of the remoted leak valve of the LV pumping system.  I turn the SEM in LV mode each night and each week-end. Interactions between the sides of the chamber and nitrogen molecules remove, each night, the contamination acquired during the day. Of course I'm also cautious of the vacuum (penning gauge) and the SEM has an airlock chamber to avoid to vent too frequently the chamber (big cause of contamination).

What SEM do you use? Most of the SEM suppliers can offer plasma cleaners for their instruments. It is worth checking these out as they are very effective at removing hydrocarbon contamination from the chamber. They can also be used as a standalone cleaner to clean microscope parts.