Advances in rapid prototyping have allowed for the construction of biocompatible materials (hydrogels) to be used in regenerative medicine. Within this area of construction inherent problems arise due to the mechanical instability of such materials that are temperature dependent. This research paper describes a thermal imaging analysis used to circumvent needle blockage when using an RP technology called bioplotting, used for extruding high temperature hydrogels, where agarose was the experimental biomaterial. The investigation describes how we have overcome these inherent problems through thermal imaging analysis, allowing us to accurately construct 3D biological matrices that have satisfied the in-vitro cell requirements for producing artificial tissue scaffolds. By properly insulating the needle and chamber, we have reduced the time taken for the needle to reach a sufficient plotting temperature. The analysis has allowed us to produce 3D biological matrices that have satisfied the in vitro cell requirements for producing artificial tissue. The analysis reported in this paper has opened the possibility for other high temperature dependent hydrogels to be constructed into 3D biological matrices without delay.