This paper presents the optimized design, fabrication and thermal characteristics of micro-heaters for thermal MEMS (micro electro mechanical system) applications using SDB and SOI membranes and trench structures. The micro-heater is based on a thermal measurement principle and contains for thermal isolation regions a 10 micrometers thick Si membrane with oxide-filled trenches in the SOI membrane rim. The micro- heater was fabricated with Pt-RTD on the same substrate by using MgO as medium layer. The thermal characteristics of the micro-heater with the SOI membrane is 280 degree(s)C at input power 0.9 W; for the SOI membrane with 10 trenches, it is 580 degree(s)C due to reduction of the external thermal loss. Consequently, the micro-heater with trenches in SOI membrane rim provides a powerful and versatile alternative technology for improving the performance of micro-thermal sensors and actuators.