Experimental data about 3D arrangements and building modes of cyclodextrin (CD) tubes are scarce, though investigations of such assemblies are particularly interesting for a vast array of applications related to organic tubes in general. Opting for a theoretical approach, we studied the organisation of CD tubes by three schemes: a structural examination of geometries from the Cambridge Structural Database, simulated annealing studies based on classical force fields to evaluate the stability of tubular arrangements, and an incremental construction procedure of the tubes by molecular dynamics. For β-CDs, the investigations pointed to a head-to-head configuration, while γ-CDs favoured a head-to-head+tail-to-head triplet. The position and interactions of water molecules inside the obtained tubular arrangements were studied as well. Various complexes for diphenylpolyenes and styrene included in the β- and γ-CDs tubes were considered and compared based on structural, energetic and dynamic criteria.