Estimate mean amplitude in frequency range using fft
The Discrete Fourier Transform is a summation :

$$ X_k =\sum_{n=0}^{N-1}x_ne^{-j2\pi kn/N} $$

Which means, the more data you have, the bigger the output mangitude. What you can do is normalizing your output by dividing the magnitude of the result by the number of samples in your signal.

I would invite you to check this question for more details.

On a side note, you may want to consider zero padding for better peak detection accuracy. Also, if you intend to filter out the noise by suppressing the peaks that you consider noise and then do an inverse FFT, you will gain to read this other question

We could most likely help you more if you gave more details about your problem as I suggested in my comment.

Hope that helps.