Three-dimensional (3D) printing becomes an attractive technique to fabricate tissue engineering scaffolds through its high control on fabrication and repeatability using the printing parameters. This technique can be combined by the finite element method (FEM), and tissue-specific scaffolds with desirable morphological and mechanical properties can be designed and manufactured. In this study, the influential 3D printing parameters on the morphological and mechanical properties of polycaprolactone (PCL) filament and scaffold were studied experimentally and numerically. First, the effects of printing parameters and process on the properties of extruded PCL filament were investigated. Then, using FEM, the effects of filament specifications on the overall characteristics of the scaffold were evaluated. Results showed that both the printing process in terms of resting time and remaining time and the printing parameters like pressure, printing speed, and printing path length have influenced the filament properties. In addition, both the filament diameter and elastic modulus had significant effects on the properties of scaffold especially, a 20% increase in the filament diameter caused the scaffold compressive elastic modulus to rise by around 72%. It is concluded that the printing parameters and process must be tuned very well in fabricating scaffolds with the desired morphology and mechanical property.