Mechanisms for controlling the assembly of molecular arrays in carbon nanotubes via alteration of the size and geometry of the functional groups attached to the molecules inserted into the nanotubes are studied. As model compounds, a series of structurally related fullerenes functionalized with polyaryl groups (C(60)X, where X is a polyaryl group) of various lengths are synthesized to explore this effect. These molecules are inserted into single-walled carbon nanotubes (SWNTs) under mild conditions to prevent their decomposition and to form C(60)X@SNWT structures. The molecular chains thus formed are studied by high-resolution transmission electron microscopy, X-ray diffraction, and Raman spectroscopy, revealing that the functional groups increase the interfullerene separation proportionally with the size of X. However, the functional groups themselves appear to adopt various orientations with respect to each other and exhibit intermolecular pi-pi interactions within the cavities of the carbon nanotubes. All these effects create a distribution of observed interfullerene separations in nanotubes, which are examined by theoretical simulations and interpreted in terms of molecular geometries and intermolecular interactions.