Planar alignment of columnar liquid crystals was achieved in microgroove structures fabricated by a direct laser lithography using two photon polymerization. A liquid crystalline material exhibiting the columnar phase was sandwiched between a substrate with microgrooves and an untreated glass substrate, and the orientation characteristics were investigated with a polarizing optical microscope. A uniform uniaxial alignment was observed in the microgrooves, and the measurement of the optical birefringence indicated that the columnar director aligned perpendicularly to the grooves.