A part having +1.3, -1.35mm in X.0.5,-0.47mm in Y.1.7, -1.8mm in Z. How to apply shrinkage in mold, PC material. Should I use material shrinkage or apply these deflection in mold ? how to apply?

It depends on where the gate is. I would not think the flow vs. cross flow would not come into play with a part this small. Are there any big cores or steel anywhere that would cause differential shrinkage? You need to keep your stackups the same if you decide to differentially shrink the tool.

You are correct Gregg! This can be further reduce.
I have got these values from CAE. tool is yet not Produced.
I would like to know how to apply shrinkage in mold.

With such a small part, please ensure that you have a suitable screw & barrel.
For shrinkage factor, please refer to the material technical data sheet. However when fabricating/designing the tool, you will need to apply steel save measures.
Why???
When the first article is produced a measured, we can perform the necessary modifications by removing the steel. Again, please ensure you have the right sized screw & barrel.
Why???
If the screw & barrel is too big, it will degrade the material and the shrinkage will not be predictable.
Since it is PC based, we will need to dry the material using a dehumidifier. We will need to select a suitable size since we do not want to over dry the material. Over dry of material will lead to degradation of additives and impact the process performance.

Shrinkage with PC is very consistant in flow vs cross flow. Use what is recommended by the resin mfg.

Shrinkage rate is differnt from different Grade PC.
How to apply the PC? when you make the molds , the molds size should be a little bigger than the product size,will be products size*(1+its shrinkage).

such a small part, just follow the resin data sheet recommendation.

It is common practice to apply common practice to apply material shrinkage to mold!
but I am seeking method of applying different shrinkage in different direction.

If the part total dimensions are 1,3X0,5X1,7 then it is the same weather you use any shrink value at all. Unfilled PC shrink is 0,5% and that means for the longest dim (1,7) less than 0,01mm compensation in the mould.
However usually for the unfilled amorphous resins 0,5% should be used for all directions. If there is GF filling then you could use different values for directions. You should know very precisely how the part is filled (all flow directions), then you could give a guess for the compensation.
Semicrystalline resins the use of different shrink values becomes more important especially when the part is filled from one end (like long connectors). However to make good estimation requires good part and resin knowledge. I have had few case when there was necessary to use three X, six Y, two Z shrink values to get the part in to spec.
Computer based estimations are not directly useful for making the tool compensation. The nature is more complicated than the programs can calculate.