The traces are not perceived by the five external senses, but presumably by manas , the mind, acting as an internal sense. Memory plays a subsidiary but important role in perception. It qualifies the way I perceive something. My memory of other things I have perceived in the past affexts the way I perceive the same or other things now. The world we perceive is the outward aspect of the world of minute, indivisible, unchangeable, eternal atoms.
Atoms exist independently of our thoughts and our perceptions.
They are the objective reality of the material cosmos. The world of our experience, a world of things with qualities, related to each other, acting on each other and affecting each other. The world of things is real. The atoms are its ultimate constituents. They relate to and associate with each other because of the omnipresence of the all-pervading akasha, the ether, space as a kind of very fine 'stuff'.