Some observations:

t = 0:1/Fpoints:d; % this results in an array 1x101

While:

w1 = hann(16384); % results in an array 16384x1

Multiplying them together with * results in a matrix which is 16384x101. So here there is some room for improvement for sure.

I cannot really tell however what you actually want from your code currently, but let's assume the following:

• The signal is a sine wave, defined as sin(2 * pi * 5e7 * t), where t goes from 0 to N-1/Fpoints
• The hann window has the same size, and also the same layout (always remember that rows and column matter a lot for dot products and matrix multiplications)

Here's a demo for now, please tell me if this is not what you wanted to do?

N = 16384;
Fpoints = 1e9;
t = (0:N-1)/Fpoints;
w1 = hann(N)';
signal = sin(2 * pi * 5e7 * t);
windowedSignal = w1 .* signal; % w1 is a column, signal is row
figure(1);
subplot(3,1,1)
plot(t, signal)
ylabel("Signal")
xlim([0, t(end)])
subplot(3,1,2)
plot(t, w1)
xlim([0, t(end)])
ylabel("Window")
subplot(3,1,3)
plot(t, windowedSignal)
xlim([0, t(end)])
ylabel("Multiplied")