We demonstrate that amplitude modulation of a high-peak-power femtosecond laser pulse allows to change fundamentally the frequency-angular structure (FAS) of the supercontinuum formed during the filamentation in both molecular and atomic gases. Particularly, modulation with a 4-hole mask forms an inverted pattern of conical emission (CE) with its predominance in the Stokes wing of the pulse spectrum. We explain this phenomenon as a joint effect of self-phase modulation and temporal pulse splitting of interfering beamlets formed by the modulating mask. Our results pave a way for tailoring the frequency-angular structure of a filament-generated supercontinuum.