In this paper, we study the fault-tolerant metric dimension in graph theory, an important measure against failures in unique vertex identification. The metric dimension of a graph is the smallest number of vertices required to uniquely identify every other vertex based on their distances from these chosen vertices. Building on existing work, we explore fault tolerance by considering the minimal number of vertices needed to ensure that all other vertices remain uniquely identifiable even if a specified number of these vertices fails. We compute the fault-tolerant metric dimension of various chemical graphs, namely fullerenes, benzene, and polyphenyl graphs.