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A modification of the micromolding in capillaries (MIMIC) technology that allows the definition of three-dimensional (3-D) polymer microlenses is presented in this letter. In order to obtain high-quality meniscuses molds from which microlenses can be formed, microchannels defined by surfaces with identical contact angles are required. We have achieved this by using a modified SU-8 (XP SU-8 NO-2). This photoresist retains the structurability of the SU-8 (being then possible to define self-alignment structures for adequate fiber optics positioning) while having a lower refractive index than standard SU-8 (achieving light confinement by total internal reflection). Experimental measurements of the fabricated ellipsoidal microlenses have shown the two Sturm focals and the circle of least confusion. These results validate the presented modification of the MIMIC technology, with which polymer waveguides ending with 3-D microlenses and integrated self alignment structures for adequate fiber optics positioning have been defined.