Given a FIR filter $h[n]$. Its action can described as:
$$ \mathbf{y} = \mathbf{H} \mathbf{x} \\ \mathbf{y} = \mathbf{X} \mathbf{h} $$
where $\mathbf{H}$ and $\mathbf{X}$ is a Toeplitz matrix. If $h$ is unknown, Least Squares with a white Gaussian input signal $x[n]$ can be used to find the unknown coefficients:
$$ \hat{\mathbf{h}} = (\mathbf{X}^{T}\mathbf{X})^{-1} \mathbf{X}^T \mathbf{y} $$
Caveat: $x[n]$ must be white; otherwise the regression matrix $\mathbf{X}^T \mathbf{X}$ is badly conditioned.
The frequency domain information is encoded in the coefficients $h$. However, as can be seen above, the LS algorithm estimates the coefficients with zero prior knowledge; the estimation ONLY depends on the input signal $x$. It does not matter if the system to be identified is an allpass filter or has a notch of 200dB attenuation at $\pi/2$.
Now my question: What do I do if I only care about a small frequency range in $h$ and hence my input signal $x[n]$ does not need to be white?
Example: My Nyquist rate is 10kHz. My unknown system is a lowpass with -3dB at 300 Hz. It has some "weird" frequency behavior around 300 Hz which I want to estimate. I do NOT care about anything beyond, say, 500 Hz. Additionally, my measurement setup prevents me from using a white input signal. I have a bandwidth limitation of 500 Hz. I cannot change the Nyquist rate.
With Least Squares I cannot identify the system because $x$ is not white (persistently exciting). Regularization/SVD does not help me: It provides a biased solution and still gives me $h$ values that try to estimate the entire frequency range. But I really want to say "Give me the $h$ that describes the unknown system best up to 500 Hz with a 500 Hz input signal"