A range of fullerenes (C60) functionalized with long alkyl chains have been synthesized andinserted into single-walled carbon nanotubes. The impact of the alkyl chain length and of the type of linkerbetween the addend and the fullerene cage on the geometry of molecular arrays in nanotube has beenstudied by high-resolution transmission electron microscopy. In the presence of functional groups the meaninterfullerene 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.