Can I clone 2 TB External HDD To 3 TB Internal HDD ?

Yes, you should. Just make sure they are both plugged in and manually copy files across in Windows from one drive to another manually or with your software.

You can use a program like HDtune or any other one to check your new drive for bad sectors.

I've transferred 2TB across drives manually just fine several times before without any issues.

I am not sure if I understood you correctly.

I want to do this using Cloning software & not manually.

I have 4 HDD slots so no problem connecting them.

Drive with OS has the clonning software & other two drives namely 2 TB & 3 TB are both just data drives & all drives are plugged in.

Yes, it should be fine to just clone data over, you could always switch the new drive to a MBR if you'd like.

As I was saying though manually copying works great too, but you can use the cloning software.

I don't like using software to copy data(500GB or more) from one drive to another in-case it either crashes or freezes and it makes you copy everything at once.

In conclusion, go ahead and copy over the data, it should be fine; manually copying from drive to drive is a good option too to avoid issues.

Makes lot of sense.

When you say manually, you mean just copy-Paste folder by folder or use a software like robocopy or other ?

Folder by folder, for example, one of my data drives:

Data Storage(A:\) 2TB

-Folders-
Audio
Drivers and Software
Games
Images
Movie & TV

I'd do one at a time to ensure safe data transfers.

Many Thanks.