You are turning off the visibilioty very late, until then the figure is already created. What you need to do is to turn it off at creation. They following code will turn off the visibility of all figures before at creation so they will not steal focus. And when the processing is done, the final for loop will turn on the visibility again
num = 0;
fig = cell(1, endblock);
for n = 1:endblock
fig{n} = figure('Visible', 'off');
for block = 1:endblock
name = sprintf('Idx_%d',n);
index = Sort.Sort.(name)(block).avg;
num = num + size(Sort.Sort.(name)(block).block,2);
tvec = 1:97;
avg = cell2mat(index);
plot(tvec,avg,'Color',[1 0 1/block]);
xlabel('Time (min)');
ylabel('Mean Voltage (V)');
title(['Idx' num2str(n)]);
hold on
end
legend(['Blocks = ' num2str(endblock),' Waveforms = ' num2str(num)]);
print(['Idx ' num2str(n)],'-dpng');
num = 0;
end
for i=1:length(fig)
fig{i}.Visible = 'on';
end
