We address a numerical methodology for the approximation of coarse-grained stable and unstable manifolds of saddle equilibria/stationary states of multiscale/stochastic systems for which a macroscopic description does not exist analytically in a closed form. Thus, the underlying hypothesis is that we have a detailed microscopic simulator (Monte Carlo, molecular dynamics, agent-based model etc.) that describes the dynamics of the subunits of a complex system (or a black-box large-scale simulator) but we do not have explicitly available a dynamical model in a closed form that describes the emergent coarse-grained/macroscopic dynamics. Our numerical scheme is based on the equation-free multiscale framework, and it is a three-tier procedure including (a) the convergence on the coarse-grained saddle equilibrium, (b) its coarse-grained stability analysis, and (c) the approximation of the local invariant stable and unstable manifolds; the later task is achieved by the numerical solution of a set of homological/functional equations for the coefficients of a polynomial approximation of the manifolds.