I don't have a stamp and am marking my bills with a normal pen. I have found that the best spot to mark is on the face of the bill, in the white circle area on the bottom right. Will the banks remove these notes from circulation because I am marking over a security feature? It is right in the spot where if you hold it up to the light you can see the head in the paper.
Yes and no. I say no, because others have said no. I'm not sure if their opinions are based on fact, assumption, or anecdote. I say yes, because I've never had trouble. The only bit you need to worry about stamping over are the barcodes on the reverse. I figure that as long as bill readers (the ones in candy machines, parking kiosks, etc) will accept them (and all the ones I've tried do), the banks will too. I stamp mine pretty heavily in the window (the white bit you talked about), and I know, factually, that banks have kept them in circulation. I'm sure, however, that you've started a debate…
That is the critical security feature – the "ghostly image" is the one most often checked – I would suggest avoiding it. try to avoid the bars on the back as well – they are used by the counting machines to differentiate between the banknotes. I often stamp or write on the note on the OPPOSITE side of the holographic (metallic) strip – the ink has backing then and does not interfere with he security features. the next best choice might be near the braille on the face side – top right. you are taking your chances anywhere, however, I think, after some consideration, these areas may be best.