We explore the concept of separating systems of vertex sets of graphs. A separating system of a set $X$ is a collection of subsets of $X$ such that for any pair of distinct elements in $X$, there exists a set in the separating system that contains exactly one of the two elements. A separating system of the vertex set of a graph $G$ is called a vertex-separating path (tree) system of $G$ if the elements of the separating system are paths (trees) in the graph $G$. In this paper, we focus on the size of the smallest vertex-separating path (tree) system for different types of graphs, including trees, grids, and maximal outerplanar graphs.