We use molecular dynamics simulations to investigate the water-mediated self-assembly of two amyloidogenic beta-sheets of hIAPP(22-27) peptides (NFGAIL). The initial configurations of beta-sheet pairs are packed with two different modes, forming a tube-like nanoscale channel and a slab-like 2-D confinement, respectively. For both packing modes, we observe strong water drying transitions occurring in the intersheet region with high occurrence possibilities, suggesting that the "dewetting transition"-induced collapse may play an important role in promoting the amyloid fibrils formation. However, contrary to general dewetting theory prediction, the slab-like confinement (2-D) shows stronger dewetting phenomenon than the tube-like channel (1-D). This unexpected observation is attributed to the different surface roughness caused by different packing modes. Furthermore, we demonstrated the profound influence of internal surface topology of beta-sheet pairs on the dewetting phenomenon through an in silico mutagenesis study. The present study highlights the important role of packing modes (i.e., surface roughness) in the assembly process of beta-sheets, which improves our understanding toward the molecular mechanism of the amyloid fibrils formation. In addition, our study also suggests a potential route to regulate controllably the self-assembly process of beta-sheets through mutations, which may have future applications in nanotechnology and biotechnology.