The study of the interactions among different types of interconnected systems in complex networks has attracted significant interest across many research fields. However, effective signal processing over layered networks requires topological descriptors of the intra- and cross-layers relationships that are able to disentangle the homologies of different domains, at different scales, according to the specific learning task. In this paper, we present Cell MultiComplex (CMC) spaces, which are novel topological domains for representing multiple higher-order relationships among interconnected complexes. We introduce cross-Laplacians matrices, which are algebraic descriptors of CMCs enabling the extraction of topological invariants at different scales, whether global or local, inter-layer or intra-layer. Using the eigenvectors of these cross-Laplacians as signal bases, we develop topological signal processing tools for CMC spaces. In this first study, we focus on the representation and filtering of noisy flows observed over cross-edges between different layers of CMCs to identify cross-layer hubs, i.e., key nodes on one layer controlling the others.