Advances in high-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) enable molecular-level characterization of ultracomplex asphaltene samples. Such analyses most often reveal compounds that are highly aromatic but alkyl-deficient in nature and, thus, support the classical "island" model of asphaltene architecture. However, recent works that combine chromatographic separations with mass spectrometry for the analysis of crude oils have shown that differences in ionization may greatly affect the analysis of complex mixtures (known as the matrix effect). Simply, compounds that ionize with greater efficiency are preferentially observed and mask the detection of poorly ionized compounds. Asphaltenes are not immune to this phenomenon. In the first of this series (10.1021/acs.energyfuels.7b02873), it was demonstrated that asphaltenes generated by different precipitants showed greatly varied monomer ion yields (ionization efficiencies). This work focuses on the development of an extrography fractionation method that selectively targets the removal of asphaltene species that exhibit high monomer ion yields and, thus, restrict mass spectral characterization of less efficiently ionized species. Silica gel was used as the stationary phase, and a unique solvent series separated asphaltenes based on their interaction with the silica surface, which was later determined to depend heavily upon the structure as well as monomer ion yield. The first two solvents (acetone and acetonitrile) isolated compounds that most efficiently produce monomeric asphaltene ions and, thus, cause bias in mass spectrometric analyses of whole asphaltenes. A solvent polarity gradient was then used, with n-heptane, toluene, tetrahydrofuran, and methanol, to separate remnant asphaltene compounds on the basis of polarity and structure. Our results demonstrate that mass spectrometry of whole asphaltenes does not reveal the complete molecular composition but rather preferentially exposes highly aromatic, alkyl-deficient, island-type structures. Early eluting fractions are shown to resemble the composition of the whole asphaltene and are enriched in island structures, whereas the analysis of later-eluting fractions reveals archipelago structural motifs as well as species with atypical asphaltene molecular compositions. We also demonstrate that, as molecular weight increases, the asphaltenes exhibit increased contributions of archipelago structural motifs. Higher mass ions (m/z > 550), even from asphaltene fractions enriched in island structures, exhibit fragmentation pathways that originate from archipelago structures. Thus, positive-ion atmospheric pressure photoionization (APPI) FT-ICR MS provides molecular-level data that suggest that the island model is not the dominant structure of asphaltenes. It coexists with abundant archipelago structures, and the ratios of each are sample-dependent.