In this work we demonstrate a significant advance in the introduction of embedded defects in 3D photonic crystals by means of two-photon polymerization. We have developed the ability to precisely position embedded defects with respect to the lattice of 3D photonic crystals by imaging the structure concurrently with two-photon writing. Defects are written with near-perfect lattice registration and at specifically defined depths within the crystal. The effect of precise defect position on the optical response is investigated for embedded planar cavities written in a photonic crystal. The experimental data are compared to spectra calculated using the Scalar Wave Approximation (SWA).