Make a binary image mapping out the pixels less than some threshold and then use that as a logical index to set them to zero:
thresholdValue = 100; % Or whatever you want
belowThreshold = grayImage < thresholdValue; % Create binary image.
% Make a copy that will be masked.
newImage = grayImage; % Create a copy.
newImage(belowThreshold) = 0; % Assign them to zero.