Many students get confused beteen 'make' and 'do' although there are exceptions, the general rule is we use 'do' for actions and 'make' when we create something.
But in the case of 'notes' the action is to 'take' notes not 'do'. 'Take notes' generally refers to writing down the basics of what you hear whilst at a lecture or interview etc. '
You can also use 'make notes'. The concept of this is to create notes that represent, in your own words, a summary of what you have read, heard or thought about. You don't need to be listening to someone else to 'make notes', but you do to 'takes notes'.