The composite attachment loss during orthodontic clear aligner therapy is an adverse event that commonly happens in clinical practice and can affect the overall outcome and length of treatment. The aim of our research is to provide a basis for the further study of an innovative digital protocol and application method for orthodontic aligner attachments. Two 3D models were designed, one based on the proposed protocol and the other on the conventional method for aligner attachment application. Four attachment shapes were used to identify the maximum values for the von Mises equivalent stresses, the maximum displacements values and the areas in which these values were recorded through FEM analysis. The results of the mechanical simulation show lower values of von Mises stress recorded in the 3D printed attachments assemblies, independent of their shape, when simulated under the same boundary and load conditions. The trapezoidal prism shaped 3D printed model has a 3.7 times smaller displacement value (0.088 [mm]) compared to the adhesive resin model (0.326 [mm]). In conclusion, the proposed protocol for aligner attachments and the introduction of innovative materials is a promising method of solving conventional attachment problems in current orthodontic treatments.