One of the major advantages of stencil lithography is the possibility to use stencils many times. However, when stencils contain nanoapertures, the clogging of the membranes limits the useful life time of the stencils. The clogging is due to the accumulation of material deposited inside the apertures of the stencil. Here, we report a study on the effect of the clogging on the life time of stencils after Al depositions through the stencils. Then we present a method to clean the stencils based on Al wet etching to eliminate the clogging. We show that this method allows the reusability of stencils for the repeatable depositions of Al nanostructures.