How can I transfer my games from the system memory to my micro SD card?

After further research it seems that direct transfer from system to micro-SD is not possible and you have to re-download games.

See quote from official Nintendo site below:

Software data cannot be moved from the console's system memory to the microSD card.

If you'd like to store software data on the microSD card, you must first delete the data from the console's system memory. Then, open Nintendo eShop and redownload the data to the microSD card.

Source

In v10.0.0, it is now possible to move data between the internal system storage and microSD card without having to go through the hoops provided in the previous answer.

To do this, simply go to System Settings. Under the Data Management menu, the option to "Move Data Between System / microSD" card will be available.

Users can now transfer downloadable software, update data, and DLC from the system memory to an SD card (and vice versa).

Note that save data and some update data cannot be transferred to an SD card.