Optimal tip sonication settings, namely tip position, input power, and pulse durations, are necessary to ensure proper mixing and maintain solution temperature below a critical temperature. This is significant for temperature sensitive procedures like preparation of viable cell extract for in vitro protein synthesis. In this paper, the optimum tip immersion depth is estimated which ensures maximum mixing thereby enhancing thermal dissipation of local cavitation hotspots inside the sonication tube; from modeled velocity field streamlines this is found at immersion depths between 20-30% height below the liquid surface. A simplified finite element (FE) heat transfer model is presented and validated experimentally with (R2 > 97%) which can predict the temperature rise over time in a tip-sonicated vessel. This model is used to observe the effect of temperature rise on cell extract performance of E. coli BL21 DE3 star strain and estimate the temperature threshold. From the combined heat map of yield and temperature it is observed that yield is correlated with final steady state temperature. Relative yields in the top 10% are observed for solution temperatures maintained below 32°C; this reduces below 50% relative yield at temperatures above 47°C. To extend utility of these finite element models to other temperature sensitive sonication processes, we also present a generalized workflow for direct simulation using the FE code as well as master plots for estimation of sonication parameters (power input and pulse settings) without need of running the code.