A range of fullerenes (C-60) functionalized with long alkyl chains have been synthesized and inserted into single-walled carbon nanotubes. The impact of the alkyl chain length and of the type of linker between the addend and the fullerene cage on the geometry of molecular arrays in nanotube has been studied by high-resolution transmission electron microscopy. In the presence of functional groups the mean interfullerene separations are significantly increased by 2-8 nm depending on the length of the alkyl chain, but the periodicity of the fullerene arrays is disrupted due to the conformational flexibility of the alkyl groups.