What do you mean by "nano" ? Remember that graphite is highly anisotropic, especially at small scale, so that your pores probably also need to be highly anisotropic (slit-shaped) for being filled. However, graphite is a soft material so that clogging pores by spreading graphite at the surface should be possible.
I can imagine two main strategies: 1. filling the pores with graphite, 2. filling the pores with a graphite precursor like PANI and carbonizing it.
Both goals are hard to achieve: the first one seems to require either an extraordinary stable nanomaterial, so that you can apply pressure to force the grapite in, or extremely favorable surface properties of your start material which should have an excellent wetting with the graphite. In the latter case, the infiltration might be possible by using an agitated slurry. The graphite must be very fine nanopowder to fit into the pores. The second option might be to fill the pores with an organic precursor, e.g. a polymer, which is carbonized later on. This might be done by filling with a soft polymer or by doing the polymerization directly in the pores. However, getting graphite in nanopores is still difficult, since the graphitizing usually requires high temperatures which are expected to result in a coarsening of the start nanostructure. In the very special case that the polymer precursor and the graphite have very excellent wetting with your starting material (to stabilize the interface strongly) the coarsening might be suppressed. But even then, a dense filling is difficult to achieve since during the graphitizing of polymers, gases like N2 and CO or CO2 have to escape.