OK I am reaching out to the metal working people here. I need an education in end mill bits. Let the class begin. :glasses-nerdy:
I am eventually getting back into my shop. I am almost sure of this.
As I have been away from my friends in the shop I have had many ideas float across my brain waves. Some I have been able to capture.

I have some ideas to make some pen blanks from aluminum. Do not have a metal lathe and probably never will. But I believe I can do what I want to with a wood lathe. My question is this. I have carbide router bits and that is all I use. Good quality. I want to drill and also route grooves in the aluminum.
Would it be better to get a mill bit to do this?
I drill aluminum with regular drill bits. Grooves could be made with end mills, but other tooling may be a better choice depending on what you are planning. I don't buy aluminum specific end mills, but speed and feed are important to get good results and reasonable tools life.
Can a mill bit be used in a router--- what is the shaft sizes.
I use end mills in routers all the time for wood. For pen size projects I like 1/8" shank mills. There is a wide selection of shank sizes and you will be able to find something that will work with whatever collets you have. Routers spin a little too fast for aluminum in my opinion, but it can be done if you don't care about tool life or cut quality. Handholding the router with aluminum is not something I would recommend.
What is the smallest bits I can get?
The smallest I've used had a 0.001" tip (a 10 degree engraving bit). You can get end mills really really small (lots of micro tooling available). Being able to do anything with them without breaking them is another story.
Where is a good place to get them?
Enco sells reasonable quality general purpose carbide end mills for the home shop. I wait and buy when they have sales (pretty frequent). There are a number of tool makers that sell really nice end mills at astronomical prices. You might want to wait until you get that Boeing contract before ordering any of those though. :biggrin:
What is the advantage if any of a mill bit over a router bit?
I've gotten good results with end mills on wood. I have not gotten good results with router bits on aluminum. The cutting angles and chip clearance on router bits aren't optimized for metal.
What precautions need to be taken?
Any vibration will quickly result in broken bits. Feeds and speeds are critical for cut quality and bit life. Hand holding a router will result in a lot of broken bits (and maybe worse problems) and lousy cuts. Aluminum powder is flammable and conductive. If you are generating dust because you are using the wrong speeds / feeds, you are looking for trouble. Aluminum chips bouncing into an electrical outlet can get exciting. Don't leave power strips laying around near your work area. Metal chips are sharp and shiny. They will get tracked in the house at some point. If you don't live alone, your better half may find metal chips a couple orders of magnitude more annoying than wood chips.
Is there a huge difference in the amount of flutes per bit and what is optimal?
What is optimal will depend on what you are trying to do. More flutes requires higher feed / lower speed to avoid burning up the bit. Too much feed breaks the bit. I use 4 flute end mills on wood and really high feed and speeds. I use 2 flute end mills on my mill on metal more than I use 4 flute end mills. I use 1 flute engraving bits on my mill on metals and resins more than anything else.
Thanks to all the teachers beforehand and no there will be no apples given out.