In any case, the context (a facial expression, a gesture, a situation in general) should indicate what exactly you mean.
Here's my observation, which you can use in your practice: a Definite voice (Perfect, Continuous, Perfect Continuous), as opposed to Indefinite (or Simple, for that matter), after a modal verb will indicate the epistemic meaning of the modal. For example, "You must have done the job" will be interpreted as "I think that you have done the job"; "You will have heard the news" will mean "I take it you have already heard the news"; "He may be writing a test" will mean "Probably, he is writing a test at the moment", etc.
That is, at least in most cases it will be so.
Anyway, a language is not speaking the right words, but the ability to to verbally express yourself... and to understand what you are being told.