Semiconductor nanocrystals are a promising class of materials for a variety of novel optoelectronic devices, since many of their properties, such as the electronic gap and conductivity, can be controlled. Much of this control is achieved via the organic ligand shell, through control of the size of the nanocrystal and the distance to other objects. We here simulate ligand-coated CdSe nanocrystals using atomistic molecular dynamics, allowing for the resolution of novel structural details about the ligand shell. We show that the ligands on the surface can lie flat to form a highly anisotropic “wet hair” layer as opposed to the “spiky ball” appearance typically considered. We discuss how this can give rise to a dot-to-dot packing distance of one ligand length since the thickness of the ligand shell is reduced to approximately one-half of the ligand length for the system sizes considered here; these distances imply that energy and charge transfer rates between dots and nearby objects will be enhanced due to the thinner-than-expected ligand shell. Our model predicts a non-linear scaling of ligand shell thickness as the ligands transition from “spiky” to “wet hair”. We verify this scaling using transmission electron microscopy on a PbS nanoarray, confirming that this theory gives a qualitatively correct picture of the ligand shell thickness of colloidal quantum dots.