For the absolute highest quality photometry flat frames must be used to calibrate your image. A flat frame compensates for obstructions, reflections, and other problems in the light path. This is the path light travels from the time it enters the telescope to the moment it strikes the CCD chip. Dust on optical surfaces, reflections from baffles or poorly aligned optics, vignetting, and other noise sources can interfere with your final data.
The first thing you have to do is take flat darks. These are dark frames taken to be applied to the flats. So you want to match the integration time with that of your flat, not that of your final image. These darks will be separate from your image calibration darks. Other than that, the procedure is exactly the same as above.
The goal is to take an image of a uniform light source (the "flat" field). So the first thing you need is that uniform light source. This is the most difficult part of taking flats. The good news is that once you find a uniform light source that works you can use it forever. There is no fool-proof method of creating the uniform field. How you do it will likely depend on your physical location, mechanical ability (handyman factor) and your level of patience!
Once you have a uniform field, expose your CCD to about 1/2 of the full well depth of your pixels. Take at least 16 flat field images, this is the lowest number required in order to avoid adding noise to your final calibrated image. For .01 mag accuracy photometry keep your signal to noise ratio to 500:1 or better. The exposure time will differ based on what filter you are using since each will pass a different fraction of the light source.
Every time you change an element in the light path, such as removing a filter, you change the light path so you have to take new flats. So you can't take a flat with a V filter, then take it off and put on an R. When you do that the V filter flats should be discarded. (If you are using a high quality filter wheel then you can do all the flats at once since their orientation in the light path will be the same when the filter wheel changes it.)
- Average all your flats
- Average or median combine all your darks made specifically for the flats
- Subtract the averaged dark from the averaged flat
What you have left is your master flat. Congratulations! This flat will be good as long as you don't change anything in the optical configuration of your system.
Now you can begin taking data (images). Divide the flat into each image after you have dark subtracted it. Most software programs have a way of automatically doing this. Now your images are fully calibrated.