Background: To evaluate femtosecond laser interaction with the applanation lens during pre-programmed penetrating keratoplasty corneal cuts. Methods: Three different-shaped penetrating keratoplasty dissections were performed on edematous corneas from bank eyes using a clinical femtosecond laser system (Intralase FS60) with energies higher than 2 μJ, and the “depth into glass” parameter at 50 μm, which is defined as the length over which the laser interacts with the glass of the applanation cone in contact with the cornea. Additional full-thickness corneal incisionswere obtainedwith an experimental laser sourcewith technical characteristics similar to the clinical laser. Following cutting, tissue sections were examined by optical microscopy (OM), transmission electron microscopy (TEM), and electron energy loss spectroscopy (EELS). After the procedure, the cones were examined by optical and scanning electron microscopy (SEM). A control was obtained by repeating the procedures and stopping the laser at the cornea–lens interface. Results: OM and TEM analysis of the tissue showed the presence of solid particles of a maximum dimension of 1.5 μm on the epithelium and the anterior stroma, regardless of the laser system used to cut. The EELS technique revealed their composition as silicon dioxide. We believe that the fragments originate from the applanation cone, which is machined by the laser interacting with the glass in contact with cornea. This is consistent with the structures observed on the lens by OM and SEM. Radial and circumferential tracks on the surface of the lens are visible, corresponding to the laser path in penetrating keratoplasty protocols. No particles were found in the control samples. Conclusions: When performing penetrating keratoplasty corneal cuts by infra-red femtosecond laser, the applanation lens in contact with the cornea is machined by the laser depending on the system parameters. As a consequence, microscopic glass fragments are created, which may remain in the tissue. This unwanted effect can be avoided by opping the procedure at the lens-cornea interface.