This paper addresses the issue of production of charm or bottom quarks in association with a high pT process in hadron hadron collision. These quarks can be produced either as part of the hard scattering process or as a remnant from the structure functions. The latter sums terms of the type (alpha_s log(pT/mq))n. If structure functions of charm or bottom quarks are used together with a hard process which also allows production of these quarks double counting occurs. This paper describes the correct procedure and provides two examples of its implimentation in single top and Drell-Yan at the LHC.