Anodising

Will you be using a kit?
Paraffin wax, hmm - it should withstand the etch, desmut, anodise and dye stages if the anodise isn't too hot - the seal stage might be a problem though, as the water might have some dye in it and the temperature will be high, might give some faint cosmetic stains. Worth a try though I'd say. If you use a hot water seal and a high melting point wax I'd guess it would help.
Do you mean not colour? That's trickier, not to get stains on the uncoloured anodised parts. An unsealed anodised surface is highly absorbent and I doubt you would successfully get the wax off. Latex might do it - one chap I know used cow gum, easy to remove, but I can't remember exactly what for and what parts of the process it went through.
In rough order of importance:
[] Clean thoroughly. You should not touch the cleaned parts with anything at all after cleaning - not even cotton gloves - so attach the wires before the final cleaning and handle only by the wires - you may need a frame.
Considerably more than half the price charged for professional anodising is actually for cleaning and handling - the importance of cleaning is often underestimated.
[] Run through the entire process with some scrap bits of the same alloy(s) you will be anodising.
[] Use aluminium (difficult to get a good connection) or titanium for the frames and the wire to attach to the current - not copper! Titanium is used professionally as it can be reused more easily - aluminium frames get anodised and then you can't attach the current. Also titanium retains it's springiness, by which the parts are held in place on the frame.
[] Use the proper dye - there used to be a chap on uk ebay who sold it, but he seems to have gone, however there is a chap on german ebay, Seller: electronic-thingks see Item number: 6056354483 - he also sells titanium wire. I haven't dealt with him, but his prices seem reasonable. Don't pay germans by bank transfer though, it costs a lot.
Using the proper dye is especially important with black. If you need to deepen the black after you have gotten it as dark as you can, dye again (or dye first is better) with yellow.
[] A warm seal gives the best surface - deionised water at 70 centigrade for 30-40 minutes. However this may leach out the dye, and if so a steam seal is a good compromise. Steam for 10-20 minutes after dyeing to seal the holes. A domestic steamer will do for small parts, but it will probably stain - don't use the missus's best one...
A large professional system might go like this:
1) inspection, mechanical cleaning 2) load in frames 2a) degrease 2b) degrease recovery 2c) rinse 2d) rinse 3) etch 4) etchant recovery 5) rinse 6) rinse 7) desmut 8) desmut recovery 9) rinse 10) rinse 11) anodise 12) anodising recovery 13) rinse 14) rinse 15) dye 16) dye recovery 17) rinse 18) rinse 19) seal 20) warm rinse 21) air dry 22) visual inspection, tests for the thickness and porosity of the layer.
Some or all of the rinses are done in deionised water. The recovery stages are partly to conserve the reagents, but also to minimise contamination of the expensive rinse water.
There are five or six main processes after loading in frames - degrease, etch, desmut, anodise, dye and seal. Degreasing is used partly to keep the etch clean - etches will usually attack grease. Degreasing is not done very often.
For the home anodiser, only etch, anodise, (dye), and seal are essential. Desmut is only needed on some alloys. You can do a combined etch and desmut using an acid etch.
A brief description of the process may help - the surface is cleaned, then etched. Desmut gets rid of any non-aluminium metals from the alloy on the surface which might interfere, and leaves a mostly-pure aluminium surface.
Anodising grows a layer of aluminium oxide - this is slightly smaller than the underlying aluminium and fractures into adherent flakes which look like old threepenny bits under a microscope, with gaps between. The threepenny bits themselves are also porous.
As you may imagine, this surface will pick up dirt, grease from fingers, and so on like almost nothing else. It is highly absorbent.
Dye gets into the gaps and into the pores, then the dye rinses take some of the dye back, mostly from the gaps. The dye should stick to the oxide, but it doesn't do that terribly well.
In sealing the oxide is then partly converted to aluminium hydroxide*, which is larger than the underlying aluminium - the threepenny bits swell up and the gaps close, and the pores close too. This is now the impervious surface of an anodised part.
BTW this is all for type III sulphuric acid anodising, the most common type - there are other types but they are not really do-able at home.

Not for the anodising - I have access to chemicals through work so its no problem.
I am building the microscope from the kit - mainly to get the lenses, graticule and eyepiece - the rest is just a soft MT2 arbor a couple of bits of aluminium rod and some tiny screws.
Many thanks for all the information. I guess I'll give it a try and see what happens. Its really only a matter of getting the insides of the tubes black to avoid reflection - everything else is cosmetic.
Thanks again

Why not use matt black paint like they use in cameras etc? You could use the proper stuff from camera repair specialists, or experiment with matt modelling enamel.
cheers, David