1. An advanced process control (APC) system, comprising: a process tool for processing a plurality of historical workpieces in accordance with a plurality of sets of historical process data, and performing a plurality of process runs on a plurality of workpieces in accordance with a plurality of sets of process data; a metrology tool for measuring said historical workpieces and a plurality of sampling workpieces selected from said workpieces, thereby providing a plurality of historical measurement data of said historical workpieces and a plurality of actual measurement values of said sampling workpieces which have been processed in said process runs; a virtual metrology (VM) module for providing a plurality of virtual metrology values of said process runs by inputting said sets of process data into a conjecture model, wherein said conjecture model is built in accordance with a conjecture algorithm by using said sets of historical process data and said historical measurement values corresponding thereto, wherein said historical measurement values are the measurement values of said historical workpieces which are manufactured in accordance with said sets of historical process data, respectively; a reliance index (RI) module for generating respective reliance indexes (RI) of said process runs, wherein each of said reliance indexes (RI) corresponding to the process run is generated by calculating the overlap area between the statistical distribution of the virtual metrology value of the workpiece and the statistical distribution of a reference prediction value of the workpiece, wherein said reference prediction value of the process run is generated by inputting the set of process data of the workpiece into a reference model, wherein said reference model is built in accordance with a reference algorithm by using said sets of historical process data and said historical measurement values corresponding thereto, and said conjecture algorithm is different from said reference algorithm, and the reliance index is higher when the overlap area is larger, representing that the reliance level of the virtual metrology value corresponding to the reliance index is higher; a run-to-run (R2R) controller for controlling said process tool to perform said process runs in accordance with the following relationships: 
 u z+1 = g ( G 1,1 , G 1,2 ,. .. G 1,i , y z ); 
 u k+1 = g ( G 2,1 , G 2,2 ,. .. G 2,i ,Å· k ); 
 G 2,i = f ( RI k )Ã— G 1,i; where G 2,i =0 or Å· kâˆ’1 but not Å· k is adopted for tuning said R2R controller, if R k <RI T ; 
 f ( RI k )= RI k , if RI k â‰§RI T and k â‰¦C; 
 f ( RI k )=1 âˆ’RI k , if RI k â‰§RI T and k >C; wherein y z represents the actual measurement value of the sampling workpiece which has been processed in the z th process run; Î¼hd z+ 1 represents the control action of the (z+1) th process run when y z is adopted; G 1,i , represents the controller gain used in said R2R controller when y z is adopted, wherein i represents the number of the controller gains used in said R2R controller; Å· k represents the virtual metrology value of the workpiece which has been processed in the k th process run; u k+1 represents the control action of the (k+1) th process run when Å· k is adopted; G 2,i , represents the controller gain used in said R2R controller when Å· k is adopted; RI k represents the reliance index (RI) of the kth process run : RI T represents the RI threshold value based on the maximal tolerable error limit defined by the errors of the virtual metrology values obtained from said conjecture model; and C stands for a predetermined number of process runs.