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How do you machine countersink when there is not enough clearance for the micro stop?

There are a couple of ways. If you have a cutter you can chuck up in a drill, use that. Or, alternatively, you can use one of the deburring bits that has a hex shank, use that to slowly work your way to the requisite depth. I use one of these from Cleaveland

https://www.cleavelandtool.com/collections/drilling-and-deburring/products/3-hex-deburring-tool

for this type of countersinking. They make dedicated countersink bits you can use in a drill as well. It's also possible to remove the cage from the microstop and use it for a bit holder. Just go slow, and periodically check your depth with a rivet or dimpled coupon, whichever is appropriate.
 
Drill extension

I use a threaded drill extension to hold the cutter and turn it with a cordless drill on low speed. Cut a little, test with the rivet, cut a little bit more, until it is right.
Or, put the cutter in a drill press that has a depth stop and set the depth first on a piece of scrap.
 
You can also cut off 1/2 of the cage of the microstop basket. This will allow you to get quite close to a vertical structure that may be interfearing with the full circle basket.
 
Have done all the things others have suggested.

One of VAF advertisers had a small diameter countersink cage on sale as a Christmas special a few years ago and it works great in many reduced clearance areas. (IIRC, I paid about 1/2 the price it now sells for.)

CC01-EF38-USA.jpg
 
I use a cutter without a cage when there's no room for it. I bought a couple of old CS cages from Boeing Surplus years ago. I took the arbor out of the cage. These have several uses.

I just make extra sure I'm perpendicular to the work piece and just take a little bit at a time.

Its not perfect. But, its good enough. All you need to do to confirm that is to go look at some of the certified airplanes out there.
 
Reverse countersink tool - very cool !

Anyway, countersinking without a microstop be very careful with the single flute cutters they will dig in quickly. 3 flute cutters are a little more gentle. This would assume working with a drill and eyeballing depth…
 
I’m fortunate to have a couple RV-6 and 7 builders at my field to get tips and tool tricks from.
 

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Reverse countersink tool - very cool !

Anyway, countersinking without a microstop be very careful with the single flute cutters they will dig in quickly. 3 flute cutters are a little more gentle. This would assume working with a drill and eyeballing depth…

Easy enough to do, with a few practice holes on scrap. Just look at the diameter of the test pieces. The single flute will not chatter, unlike the multi cutter types.

Hand cutting is the least risky, just don't get in a hurry, unless you have a hundred to do. Then make a buy or make a tool. $$$ beats labor hours.
 
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Just be sure, when ordering, that you pay attention to the countersink angle. Aviation hardware is typically 50°.
I would use a 100 degree countersink for 426 rivets. What would use a 50 degree. C/S for?
 
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