Patterned carbon nanotube (CNT) arrays have been synthesized on patterned substrates created via pulsed laser deposition (PLD) of the precursor catalyst films with a mask. Arrays of CNTs in square and hexagonal patterns with tube lengths of 8 μm and 16 μm were created on silicon or quartz substrates, respectively. Using the method of laser cutting, as-grown CNT patterns were pruned by focused He–Ne laser beam. It is found that after pruning, CNTs tend to cluster together and form welded junctions. The comparison of field emission properties of CNTs before and after pruning shows that laser modification of CNT morphologies effectively enhanced the emission currents.