Seems like you have determined what you want your threshold to be.
You can set those values to zero (or whatever the mean of your signal is), pretty easily:
x; % this is your data
xpeaks = x; % duplicate
thresh = 10; % or whatever it is
meanx = mean(x);
xpeaks(abs(x) <= threshold) = meanx;
% xpeaks will contain only the "peaks"
