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Heat transfer in linear motor driven stages for surface mounting device applications was investigated. In order to avoid the complex conjugate problem, convection heat transfer within fluid flow and conduction within solid parts were modeled and solved separately. First, film coefficients of the moving parts were evaluated from computational fluid dynamics and those of the stationary parts from the existing empirical or analytic correlations. Then, by applying these coefficients, internal and external temperatures of the linear motor parts were computed through finite element analysis. As an alternative approach, a simple one-dimensional thermal resistance model was introduced and compared with the finite element analysis. A good agreement was obtained. For validation, both analyses were compared with the measurement with respect to motor driving power. The computations agreed with the measurements within an error range of 8°C. Subsequently, the thermal resistance analysis was applied to another stage with a cooling system. The influences of some factors, such as thermal conductivity of the insulation sheet, thermal contact between the coil assembly and the mounting plate, and air-cooling or water-cooling were examined through the analysis.