Just use sprintf (or perhaps strcpy and strcat) to build the command string in a buffer, then call system with that buffer. (Make sure the buffer is allocated with enough space;
Here is a contrived example suggesting how you might build a data file, then sort it (assuming the existence of a sort utility, and Unix- or MS-DOS-style input/output redirection):
char *datafile = "file.dat";
char *sortedfile = "file.sort";
char cmdbuf[50];
FILE *fp = fopen(datafile, "w");

/* ...write to fp to build data file... */

fclose(fp);

sprintf(cmdbuf, "sort < %s > %s", datafile, sortedfile);
system(cmdbuf);

fp = fopen(sortedfile, "r");
/* ...now read sorted data from fp... */

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