For many medical laser applications, a particular beam shape is required. The output beam of a laser can be approximated by a Gaussian, higher-order Gaussian, annular or a flat-top (uniform) distribution. Here, we investigate, analytically and experimentally, the effects of laser beam shapes on the depths of penetration in treatments of any types of vascular malformation. In order to do this, the physical and optical parameters of the skin must be known and measured correctly. Using the Monte-Carlo method for seven layers of skin, a software predicting the beam propagation and intensity distribution inside of tissue has been developed in our centre. In this paper, a 15 watts copper vapour laser producing (511nm and 578 nm) for treatments of patients having PWS (Port Wine Stains) of different sizes is employed. The output beam of this laser was Gaussian. We have designed a beam homogenizer converting a Gaussian beam into flat-top distribution. Therefore, the effects of the laser irradiance beam shape (before and after beam shaping) on the depth of penetration have been investigated before people's treatments. Initially, two laser beams having Gaussian output distribution of the same power are considered. The diameter of one beam is 5mm and the other one is 10 mm. The intensity distribution of these beam inside of similar tissues are predicted and it is concluded that for deep but small size PWS the Gaussian beam having smaller beam diameter is more suitable than the larger spot size. Then, the beam intensity distribution inside of the same tissue (similar parameters) for two flat-top beams of the same power but different diameters (one is 5mm and the other is 10 mm) is calculated. It can be seen that the flat top beam of bigger spot-size has smaller penetration depth but it illuminates a larger area uniformly (suitable for large but not deep area). The depth of penetration of flat-top beam with smaller spot size is deeper but it illuminates a smaller area uniformly and is suitable for treatments of patients with small but deep PWS. Using a low power laser, we have been able to image the PWS area and roughly determine the depths of malformations. Finally, depends on the size, depth and shapes of the area the required beam shape can be chosen. A clinical protocol is developed for 25 patients and it is shown an extreme improvement in related medical procedures.