The modal verb "can" usually indicates capability or ability. When you ask someone
How can I use this tool?
you're essentially asking
How am I able to use this tool?
This is a strange question to ask, because seemingly the only answer is
Because you have hands.
As you can probably guess, this isn't the answer you're looking for.
Now, the auxiliary verb "do" in that context is only a syntactic marker. This is because the question has a verb already that indicates the action: use. We use this marker when asking a question with a verb that is not to be or an auxiliary verb.
Take the question:
Do you know where the train station is?
If I rearrange this question, it is clear what it is asking (though this is not English word order):
You know where the train station is? (question)
This question will elicit the response someone wants to hear.
Now that we've covered do vs. can, we need to make the distinction between
How do you use this tool?
How do I use this tool?
I think that in your case, either sentence would be fine. Both of them are correct. It all depends on context: sometimes people actually ask these questions so that they can do something, and sometimes they just ask out of interest, with no such intent whatsoever. Allow me to be picky, however: I personally think that if you want someone to show you how to use the tool, it would be best to say
How do you use this tool?
so you can see how the person uses the tool, since you don't know how to use it in the first place. But again, I think that in your context either sentence would be fine.
To conclude: does "How can you ... ?" work when asking the question you want to ask? Here is where I run into trouble on this site. If I say no, someone will likely say "Well, people will be able to understand," which is fair. But there is a chance that someone may not understand what you mean. It all depends on how pedantic people are. "How do you ...?" will always be understood. So I think that is better to use.