The high power supercontinuum from femtosecond filamentation has attracted great attention for recent years due to its various applications. In our previous researches, we have used microlens array to obtain filament-array in fused silica and to generate the high spectral power supercontinuum. To further improve the ability to generate the high power supercontinuum by using microlens array, in this work we adopt flattened femtosecond laser beam with a flat-top energy distribution to generate filament-array in fused silica and supercontinuum. By using a laser beam shaping system consisting of aspherical lenses, the Gaussian intensity distribution of initial femtosecond laser beam is converted into a flat-top distribution. The flattened laser beam is focused by a microlens array into a fused silica block, and consequently a filament array is formed in the block. Our experimental results show that compared with the filaments formed by a Gaussian laser beam, the filaments formed by the flattened beam have a uniform distribution and almost the same onset due to the initial uniform energy distribution across the section of the laser beam. Furthermore, the spectral stability of supercontinuum emission is used to evaluate the damage of the fused silica block. It is demonstrated that the flattened beam with a pulse energy of 1.9 mJ does not induce permanent damage to the fused silica block, while the Gaussian beam with a relatively low pulse energy of 1.46 mJ leads to the damage to the block. Therefore, a higher incident laser pulse energy is allowed in the case of flattened laser beam, and consequently stronger supercontinuum generation than in the case of the Gaussian laser beam can be expected. In our experiments, the relative spectral intensity of flattened beam generated supercontinuum in the visible range is about twice higher than that for the Gaussian beam case. The conversion efficiencies of the supercontinuum for the two kinds of laser beams are further analyzed. The conversion efficiencies are 49% and 55% for the cases of Gaussian and flattened beams respectively. In this work, we demonstrate the formation of filament array with uniform distribution in fused silica, and, as a proof of principle, we also demonstrate the high power supercontinuum generation with high conversion efficiency from the filamentation, by using flattened femtosecond laser beam as the incident laser and microlens array as the focusing element. This approach provides a way to obtain a high power femtosecond supercontinuum source which is of great importance in many applications such as some absorption spectroscopies based on coherent supercontinuum light.