The data in your MAT files doesn't match up with your example code, so I'm not 100% sure what you're trying to do, but see if this does the trick.
load('ddtable.mat')
load('startdd.mat')
result =ddtable([],:);
inds = [];
for ii = startdd % Iterate over start indices
cs = cumsum(ddtable.RAIN(ii:end)); %do cumsum over most of the rain data - we'll end up throwing away anything beyond 3.5 mm
inds3_5 = ii-1 + find(cs <= 3.5); % Find where data is below the 3.5mm threshold; adjust based on the start index.
result = [result; ddtable(inds3_5,:)]; % append data
inds = [inds; inds3_5]; % append indices
end
