Hexahydro-2H-thieno[2,3-c]pyrrole is proposed as a low molecular weight polar scaffold to construct compound libraries used in the search for new drugs. Practical syntheses of derivatives of this bicyclic scaffold were developed, based on [3 + 2] cycloaddition of the ylide generated from N-benzyl-1-methoxy-N-((trimethylsilyl)methyl)methanamine and 4-substituted 2,3-dihydrothiophene 1,1-dioxides. All of the 3-substituted hexahydro-2H-thieno[2,3-c]pyrrole 1,1-dioxide derivatives were obtained as single diastereomers. Conformational properties of the hexahydro-2H-thieno[2,3-c]pyrrole 1,1-dioxide derivatives were explored using X-ray diffraction studies. The potential of the scaffold to generate libraries of 3D-shaped molecules was demonstrated.