Pulsed laser deposition (PLD) is one of the well-established physical vapor deposition methods used for synthesis of ultra-thin layers. Especially PLD is suitable for the preparation of thin films of complex alloys and ceramics where the conservation of the stoichiometry is critical. Beside several advantages of PLD, inhomogeneity in thickness limits use of PLD in some applications. There are several approaches such as rotation of the substrate or scanning of the laser beam over the target to achieve homogenous layers. On the other hand movement and transition create further complexity in process parameters. Here we present a new approach which we call Matrix Shaped PLD to control the thickness and homogeneity of deposited layers precisely. This new approach is based on shaping of the incoming laser beam by a microlens array and a Fourier lens. The beam is split into much smaller multi-beam array over the target and this leads to a homogenous plasma formation. The uniform intensity distribution over the target yields a very uniform deposit on the substrate. This approach is used to deposit carbide and oxide thin films for biomedical applications. As a case study coating of a stent which has a complex geometry is presented briefly.