Hi Harsh,
You use the filter() method with your designed filter and your input. For example:
Design a filter with a notch at 60 Hz for data sampled at 1 kHz.
fspec = fdesign.notch('N,F0,Q,Ap',6,60,30,0.5,1000);
% design filter
d = design(fspec);
% create some data to notch filter
t = linspace(0,1,1e3);
x = cos(2*pi*60*t)+randn(size(t));
% filter the data
y = filter(d,x);
% plot the PSD of the notch filtered data
plot(psd(spectrum.periodogram,y,'Fs',1e3));
Hope that helps,
Wayne