If you were marking location, consider what you'd really be saying in English.
I brush on my teeth, wash on my face, and have breakfast every day.
When you're using で you'd indicating where the action is occurring. Consider how odd this sounds in English. It's the same in Japanese: unless there's something on your teeth that you were washingbrushing or something on your face that you were washing.
If you're using で to makemark the location of an action, you're marking the location within which the action was occurring.
図書館で本をよみました。
I read my book at the library.
You could say
台所で歯を磨いて。。。
I brushed my teeth in the kitchen and ....
If you're thinking of your teeth or your face as a tool, then the rendering in English would be to the following affect:
I brushed with my teeth, and I washed with my face....
Hopefully, you're not using your teeth as a tool for brushing something (you'll wear your teeth away and there are probably better tools available). When you're brushing your teeth, you're using a toothbrush, not your teeth.
歯ブラシで歯をみがきみしみがきました。
I brushed my teeth with a toothbrush.
And unless you're into strange sexual practices, you're probably not washing anything with your face.
ハンドタオルで顔を洗った
I washed my face with a washcloth.