You need to wear only the basic essentials to get measured. Wear your usual undergarments that you wear everyday under your clothes. Briefs are good, boxers are not because they are too fluffy and interfere with accurate measuring. Find something more conforming, but not tight.
Measuring nude is not the best solution. Some measurements run through the crotch area and that would be a bit awkward. If you normally wear a bra, you should have one on for measuring.
If you're not comfortable standing in your underwear while being measured, you can wear some clothing. A full leotard would be very good, if you have it. Search your wardrobe for items that are thin and conforming, but do not distort your body.