In a method for manufacturing a semiconductor device, fin structures each having an upper portion and a lower portion, are formed. The lower portion is embedded in an isolation insulating layer disposed over a substrate and the upper portion protrudes the isolation insulating layer. A gate dielectric layer is formed over the upper portion of each of the fin structures. A conductive layer is formed over the gate dielectric layer. A cap layer is formed over the conductive layer. An ion implantation operation is performed on the fin structures with the cap layer. The ion implantation operation is performed multiple times using different implantation angles to introduce ions into one side surface of each of the fin structures.