The Savitzky-Golay filter (Signal Processing Toolbox sgolayfilt function) is probably best for your application:
F = openfig('smooth.fig');
x = get(get(gca, 'Children'), 'XData');
y = get(get(gca, 'Children'), 'YData');
x = x(~isnan(y));
y = y(~isnan(y));
b = sgolayfilt(y, 3, fix(length(y)/2));
hold on
plot(x, b, '-r')
hold off
Experiment with the filter polynomial order and frame length to get the result you want.
