‘I want to have a high pass filter such that values above zero remain, and the amplitudes of the negative values are somehow reduced as shown in the figure’
That is not how a highpass filter works. It passes frequencies above a certain value, not amplitudes.
If you want to reduce the amplitudes of the values less than zero, experiment with this:
D = load('data.txt');
x = D(:,1);
y = D(:,2);
yr = y;
yr(y<0) = -y(y<0).^2;
figure
plot(x, y)
hold on
plot(x, yr)
hold off
grid
Other transformations (or hard limits) could also be appropriate.
