Usually, small perforations of the eardrum should heal in a few weeks after the fungal infection is treated successfully. It also depends on how long the perforations have existed and how they were caused - from self inflicted trauma or due to the fungal infection. The middle ear is always wet with normal secretions and sometimes the fungal infection is due to the dampness created due to the pre-existing small perforations. If your ear drum perforations are not healing on their own, surgery may help to close them. However, surgery should not be performed in the presence of fungal infection. The fungal infection must be treated successfully first.