What is matter? One of the major themes in Emanuel Swedenborg’s thinking is the relation between the material and the immaterial, body and soul. During all his life, as a scientist and a visionary, Swedenborg (1688–1772) pondered on these questions. How can we get knowledge about the invisible? The world beyond the scope of our senses? The issue here is to explain the cognitive foundation of his matter theory expressed in his early scientific works, written before he became a visionary and mystic. Namely, I do not want to know just what he thought, but also how. In focus is the relation between environment and cognition that gives rise to theories of nature: how we think about that we can not see; how we understand the invisible through the visible. From the known we understand the unknown. In my book The Natural Philosophy of Emanuel Swedenborg: A Study in the Conceptual Metaphors of the Mechanistic World-View (Dordrecht: Springer Verlag, 2013) I put forward a cognitive-historical approach to history of science in order to explain concept formation in science. In this paper I explain, firstly, Swedenborg’s mechanistic worldview and metaphorical way of thinking up to the year 1734, and secondly, put forward new perspective of the mechanistic philosophy of the 17th and 18th century, i.e. the cognitive metaphors of the mind and its role in the formation of scientific theories. This approach can also cast new light on Swedenborg's later spiritual philosophy and doctrine of correspondences.