3-ply refers to the amount of layers the mask has, more layers means a higher filtration capacity. 3 ply surgical medical grade face masks will provide better protection than 2 or 1 ply.
If you buy face masks online from e-Surgery you will receive a 3-ply surgical face mask that conforms to BFE (Bacterial Filtration Efficiency) 98% and Type IIR Medical Grade specification.