Multimodal focused ion beam (FIB) imaging on a polydimethylsiloxane/poly(methyl methacrylate) (PMMA)/multiwall carbon nanotube (MWCNT) electrospun composite has been applied to discriminate the phase-separated polymer blend and identify MWCNT fillers. Upon tomographic reconstruction, this discrimination has been possible through both atomic number and voltage contrast, the latter being enabled by preferential MWCNT segregation to PMMA. This study suggests that electrospinning could be affecting not only MWCNT alignment but also phase separation dynamics of immiscible polymers, yielding a porous structure throughout the fibers. This work opens the door to correlative materials science in polymer nanocomposites through FIB tomography, where voltage contrast is a main actor.