Removing a stuck screw

In the process of trying to remove a PCIe card in my ThinkPad X61 I managed to damage the slot of one of the screws. Any suggestions as to how to remove it without damaging the motherboard?
 
Carefully.

Which screw-slot? one holding the motherboard to the case, or the screw-slot that holds the PCI card to the case?

If you damaged a screw-slot that holds the PCI card to the edge of the case, you can use needle-nose vice-grip pliers to get the screw out, but you'll still have to be very careful, especially if the screwhead is round.
 
You can pick up stripped-screw bits for screwdrivers/drills for just this situation. Any hardware store should have them.
 
Can't be answered without much more detail. Is it slot or Philips or hex? Is the screw buried, or can one get to the side of it? Can one cut the head off and remove the straight screw part?

Last time I took my Mac apart (had to replace the trackpad), I stripped one screw completely, and ended up having to drill it out, and re-tap the whole for a somewhat larger screw.
 
Can't be answered without much more detail. Is it slot or Philips or hex? Is the screw buried, or can one get to the side of it? Can one cut the head off and remove the straight screw part?

It's on page 76 of the HMM for the X61 - Philips Silver M2 × 2.5 mm, wafer-head, nylon-coated.... I'll see if I can get to the side of it with some small pliers.
 
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You can get a screw out that's screwed in hard and even missing the head with either of these, as long as you can grip any part of it.
 
I managed to drill into the screw and the head came off so I can remove the PCIe card, but the stub of the screw is in the hole and I'm not sure if I can reliablly drill out the remains without damaging the motherboard. I guess a single screw would be sufficient to hold it in place...
 
Single screw on a MiniPCIe card will be fine.

Make sure you get all the metal shavings out. Especially check speaker and cpu fan for chips. The speaker magnet tends to draw chips.
 
I use Left Handed Carbide Drill Bits for problems like that. Usually, the bit, since it's spinning in the direction the machine screw needs to go to be removed, will grab the screw and take it out without drilling all the way through or even taking the head off - they come in different sizes so that wouldn't be an issue like you experienced.
 
There are also left-turning steel drills. With these you can get most stuck screws out when the drill catches.
 
You can use a smaller drill to make a hole in that screw and then with the help of a tap you can make a new screw-thread.
 
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