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 brushing or something on your face that you were washing.

If you're using で to mark 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.