A flexible milling assembly for milling an orifice through a well casing. The milling assembly can include a drive yoke, and a plurality of straight and split yoke assemblies—all linked together and to a cutter head with universal blocks that enable the components to pivot relative to each other. A string of joint tubing connected to a prime mover on the surface is used to lower the milling assembly into a well and supply the driving torque. A split shoe coupled to a guide tube is positioned within the well casing where the orifice is to be milled. The milling assembly is guided through a curved passage within the split shoe to bring the cutter head into contact with the well casing. A protector assembly can be provided to enclose and protect the milling assembly when it is tripping into and out of the well casing.