Sending serial data to Arduino from Matlab(not using support package)
Got it, instead of depending on the Serial object, i sent the line feed to arduino. All this time it has been waiting for the Line feed that never arrived.

delete(instrfindall)
s = serial('COM3', 'BaudRate', 9600); %38400
fopen(s);
pause(0.1);
text = input('enter','s');
fprintf(s,'%s\n',text,'sync');
pause(0.1);
d = fscanf(s,'%s');
pause(0.1);
delete(instrfindall)