I have three variables, two ordinals which will be X and Y and the I want the third axis to be the count. I know this can be done in R, MATLAB, Scatterplot but I dont know how to do in JMP? Pls help me out.
If so, JMP doesn't create graphs like that. The third visual dimension in a bar chart like the one linked to above actually detracts from the information being displayed by obscuring some of it. See Stephen Few's comments on these types of graphs for more.
I have the same concerns as Jeff about 3D bar charts. However if you are still interested in a 3D bar chart, try the following which uses the 3D scatterplot to simulate a 3D bar chart. It's not very pretty but it is probably more useful since you can manually rotate the plot to get a better view of what is going on.