How to use CNN to deal with a 2D regression problem?
It should even be easier than classification: you do not need the final layer.

Your input layer should have 18 nodes $(x_i,y_i,t_i)|i=1..6$

Hidden layers as you see fit (experiment with it, depending on data and results).
I would expect the best results from a fully connected layer and a 'relu' layer.

The output layer has 3 nodes $(x_7, y_7, t_7)$

Train the model.

Evaluation is just feed forward of a set of 18 values, and retrieving 3 results from the output layer nodes.