FEA codes certainly can, and are, used for this type of analysis.  The one caveat is being able to describe the convective effect of the cooling holes.  If you have convective heat transfer rates for these cooling holes, then there are several codes available on the market that can do this very thing. If, on the other hand, you are also setting up the cooling hole convection as an unknown, that becomes rather more involved. In that scenario, one may have to do a CFD-type analysis, followed by the FEA.
My presumption is that you are trying to determine the temperature distribution and then the thermal stress effects which result from this.  There are commercial codes that can do this in one step, but this is often more efficiently done as a two-step analysis: First one would determine the temperatures in the part, then one would use this output as an input for a thermal stress analysis.
The short is, your problem can be done, but the "how" depends on exactly what you are trying to accomplish (and of course what code you want to use).

We only require to detemine the temperature distribution as mould surface temperature has a bearing on the glass distribution and subsequent shrinkage, especially on square/ rectangular shaped containers with large flat panels.