Electrospun scaffolds of neat poly-ε-caprolactone (PCL), poly-ε-caprolactone/β-cyclodextrin inclusion complex (PCL/β-CD) and poly-ε-caprolactone amino derivative inclusion complex (PCL/β-CD-NH₂) were prepared by the electrospinning technique. The obtained mats were analyzed by a theoretical model using the Hartree–Fock method with an STO-3G basis set, and characterized by X-ray diffraction (XRD), field emission scanning electron microscopy (FESEM), Fourier transform infrared spectroscopy-attenuated total reflectance (FTIR-ATR), differential scanning calorimetry (DSC), confocal-Raman spectroscopy, proton nuclear magnetic resonance (¹HNMR) and contact angle measure (CA). Different mixtures of solvents, such as dimethylformamide (DMF)-tetrahydrofuran (THF), dichlormethane (DCM)-dimethyl sulfoxide (DMSO) and 2,2,2-Trifluoroethanol (TFE), were tested in the fiber preparation. The results indicate that electrospun nanofibers have a pseudorotaxane structure and when it was prepared using a 2,2,2-Trifluoroethanol (TFE) as solvent, the nanofibers were electrospun well and, with the other solvents, fibers present defects such as molten fibers and bead-like defects into the fiber structure. This work provides insights into the design of PCL/β-CD-NH₂ based scaffolds that could have applications in the biomedical field.