Try uiputfile() and let the user specify the name by typing it in:
% Get the name of the file that the user wants to save.
% Note, if you're saving an image you can use imsave() instead of uiputfile().
startingFolder = userpath % Or "pwd" or wherever you want.
defaultFileName = fullfile(startingFolder, '*.*');
[baseFileName, folder] = uiputfile(defaultFileName, 'Specify a file');
if baseFileName == 0
% User clicked the Cancel button.
return;
end
fullFileName = fullfile(folder, baseFileName)
Or you can create the filename from values of some of your variables if you use sprintf().