In modern polymer industry, there still is a room for new generations of fillers capable of enhancing the performance of composite materials. Currently, much effort is being put into a process of improving mechanical properties of elastomer materials. In this work, multiwalled carbon nanotubes (MWCNTs) and graphene nanoplatelets (GnPs) were modified with silane, titanate, or zirconate using plasma treatment, in order to apply them as fillers for styrene/butadiene rubber. Following its modification, filler surface was analyzed: Surface free energy (SFE) was measured with tensiometry, and micromorphology and chemical composition were studied with scanning electron microscopy-energy-dispersive spectroscopy (SEM-EDS), while elemental composition and bonding were assessed with X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS). Low-temperature oxygen plasma activation of MWCNT fillers leads to a significant increase in the SFE polar component, with the same effect being much weaker for GnP fillers. Grafting silanes, zirconates, and titanates on activated filler surface results in a decrease in SFE polar component-surface oxygen-containing active groups react with silane/zirconate/titanate molecules. Fillers modified in this way exhibit different micromorphology and surface chemical composition what is revealed with the SEM-EDS, ToF-SIMS, and XPS techniques. As the ultimate step, either MWCNT or GnP rubber nanocomposites were manufactured using the modified fillers with their mechanical properties and cross-link density being studied. Filler modification resulted in substantial changes both in composite performance, and in its cross-linking density. In the case of modified filler containing composites, improved tensile strength and elongation at break were observed.