the output of the neural network depends on the transfer function of the output layer, if the results are negative you probably have a transfer function like "tansig" or "purelin", I recommend that if you don't want negative values you should change the transfer function, if the answer is in the range from 0 to 1 you can change it to "logsig" or whatever function you desire :
net.Layers{end}.transferFcn='logsig';