Electrospun scaffolds of neat poly-epsilon-caprolactone (PCL), poly-epsilon-caprolactone/-cyclodextrin inclusion complex (PCL/-CD) and poly-epsilon-caprolactone amino derivative inclusion complex (PCL/-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 ((HNMR)-H-1) 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/-CD-NH2 based scaffolds that could have applications in the biomedical field.