Four [4-substituted(aryl)-piperazin-1-yl](thieno[2,3-c]pyridin-5-yl)methanones, namely, 4-(methoxyphenyl)- piperazin-1-yl](thieno[2,3-c]pyridin-5-yl)methanone (1), 4-(fluorophenyl)-piperazin-1-yl](thieno[2,3-c]pyridin-5- yl)methanone (2), 4-(methylphenyl)-piperazin-1-yl](thieno[2,3-c]pyridin-5-yl)methanone (3) and 4-(3,4- dimethylphenyl)-piperazin-1-yl](thieno[2,3-c]pyridin-5-yl)methanone (4) were synthesized and characterized by FTIR, 1H NMR and LC-MS spectroscopic techniques. The single crystals of all the compounds were grown, and their molecular & crystal structures were determined by single crystal X-Ray diffraction. The molecular structure of all the compounds features an intramolecular hydrogen bond of the type C-H…N which closes into a S(6) motif. The crystal structures of these compounds display several secondary interactions of the type C-H…O, C-H…F, C-H…π and π…π, and the combination of these interactions results in adopting different supramolecular architectures. Three different structure directing C-H…O interactions in 1 builds a three dimensional architecture, while in 2, two C-H…F and one C-H…O interactions generate a three dimensional structure. Several C-H…π interactions give additional stability to the crystal structures of 1 and 2and have no structure directing features. Unlike 1 and 2, the supramolecular structures of 3 and 4are two dimensional networks formed by a combination of C-H…O and CH… π interactions. The C-H…π interactions in 3 and 4 are structure directing in nature and extends the one dimensional architecture formed by C-H…O interactions into two dimensional.