The "instrument and machinery" he had primarily in mind were logic and methodology. He rejected the syllogistic method and the Aristotelian categories in favor of a "methodical process," he called "interpretation of nature" (45).
This approach also led to some very practical ideas about note-taking. Thus he also rejected the "tricks" of artificial memory masters and their memory palaces. They are like "tricks and antics of clowns and rope-dancers." Instead, he argued for the use of commonplace books. As he found in the fifth chapter of Book 5 of Of the dignity and Advancement of Learning,
there can hardly be anything more useful even for the old and popular sciences, than a sound help for the memory; that is a good and learned Digest of common Places ... I hold diligence and labour in the entry of common places to be a matter of great use and support in studying; as that which supplies matter to invention, and contracts the sight of the judgment to a point. But yer it is true that of the methods and frameworks of commonplaces which I have hitherto seen, there is none of any worth, all of them carrying in their titles merely the face of a school and not of a world; and using vulgar and pedantical divisions, not such a pierce to the pith an heart of things.
And in a letter to o Fulke Greville, who was looking to hire assistants to help him in his research, he wrote around 1599:
He that shall out of his own Reading gather for the use of another must (as I think) do it be Epitome, or Abridgment, or under Heads and Common Places. Epitomes also may be of 2 sorts: of any one Art, or part of Knowledge out of many Books; or of one Book by itself. Of the first kind we have many Patterns; as for Civil Law, Justinian; Littleton for our own; Ramus Logick; Valerius Physicks; Lipsius Politicks, and Machivels  Art of War. some in every kind and diverse in som one. In matter of Story I will not cite Carion, Functius, Melanchthon, nor the French Bibliotheque Historien; because they are rather calendars to direct a man to Stories, than Abridgments of Story. But the reading of the best of these ... will no more make a Man a good ... Lawyer, Logician ...And if the Works of so excellent Men be so fruitless, what shall their Abridgements be?” 
General abridgments made by someone else may give us some vague ideas, but not solid knowledge. Instead, he argued:
I hold Collections under Heads & Common Places of far more profit, and use; because they have in them a kind of Observation; without the which neither long Life breeds Experience, nor great Reading great Knowledge: For id demum scimus, cujus causam scimus.(Quoted in accordance with Vernon Snow, "Francis Bacon’s Advice to Fulke Greville on Research Techniques," Huntington Library Quarterly 23 (1959-60), 369-78).
Bacon felt that commonplace books might be useful instruments of the mind, especially if the commonplaces are collected from the nature of the world, and not from the concepts of Aristotelian philosophy. In fact, for Bacon the commonplace book is not a means of storing stock phrases and ideas in accordance with traditional "commonplaces," but a tool in the discovery of a new "interpretation of nature." It is for him not a "top-down," but a "bottom-up" approach that "arrives at the most general axioms last of all" (New Organon, 43). This is "the true way," which remained "untried," but which he recommended.
Some people still use commonplace books this way. Others are trying to adapt electronic note-taking tools to this traditional approach, even though there are much better ways to keep one's notes today.