Biopolymers based on the amniotic membrane compare favorably with synthetic materials in that, along with a specific 2D structure, they have biologically active properties. However, in recent years, there has been a tendency to perform decellularization of the biomaterial during the preparation of the scaffold. In this study, we studied the microstructure of 157 samples and identified individual biological components in the manufacture of a medical biopolymer from an amniotic membrane using various methods. Group 1 had 55 samples, and the amniotic membrane was impregnated with glycerol and dried over silica gel. Group 2 had 48 samples, and the decellularized amniotic membrane was impregnated with glycerol followed by lyophilization, Group 3 had 44 samples, and the decellularized amniotic membrane without pre-impregnation with glycerol was subjected to lyophilization. Decellularization was performed by treatment with a low-frequency ultrasound at a frequency of 24-40 kHz in an ultrasonic bath. A morphological study using a light microscope and a scanning electron microscope showed the preservation of the structure of the biomaterial and more complete decellularization in samples subjected to lyophilization without prior impregnation with glycerol. The study of the Raman spectroscopy lines of a biopolymer made from a lyophilized amniotic membrane without preliminary impregnation with glycerin showed significant differences in the intensity of the spectral lines of amides, glycogen, and proline. Additionally, in these samples, the spectral lines of Raman scattering the characteristic of glycerol were not visualized; therefore, only biological substances characteristic of the native amniotic membrane have been preserved.