First, you should remove the softmax layer and change the output layer to use the MSE cost function.
The last layer before the output layer will usually be a 'reshape' layer to match the output size you are expecting.
See autoEnc.conf file for regression example. This conf file is a part of the AutoEnc demo (autoencoder), try to follow the network structure and training.
In the doc file there are some explanation on how to run regression, section 3