As proecsm points out, your data needs to be made into columns. Like this:
x = 1:1000; %Row vector
y = sin(0.01*x) + cos(0.03*x) + 0.1*randn(size(x)); %Row vector
F = fit(x(:),y(:),'fourier3') %Use (:) to turn it into a column
plot(x,y)
hold on
plot(F)
Also, are you aware of the Curve Fitting Tool GUI?
cftool
This makes it easier to try out different fits interactively (for both curves and surfaces), and you can automatically generate MATLAB code from your results.
