  In the last decade ground based high resolution Doppler spectroscopy (HRS)
has detected numerous species in transiting and non-transiting hot Jupiters,
and is ideally placed for atmospheric characterisation of warm Neptunes and
super Earths. Many of these cooler and smaller exoplanets have shown cloudy
atmospheres from low resolution near infrared observations, making constraints
on chemical species difficult. We investigate how HRS can improve on these
given its sensitivity to spectral line cores which probe higher altitudes above
the clouds. We model transmission spectra for the warm Neptune GJ~3470~b and
determine the detectability of H$_2$O with the CARMENES, GIANO and SPIRou
spectrographs. We also model a grid of spectra for another warm Neptune,
GJ~436~b, over a range of cloud-top pressure and H$_2$O abundance. We show
H$_2$O is detectable for both planets with modest observational time and that
the high H$_2$O abundance-high cloud deck degeneracy is broken with HRS.
However, meaningful constraints on abundance and cloud-top pressure are only
possible in the high metallicity scenario. We also show that detections of
CH$_4$ and NH$_3$ are possible from cloudy models of GJ~436~b. Lastly, we show
how the presence of the Earth's transmission spectrum hinders the detection of
H$_2$O for the most cloudy scenarios given that telluric absorption overlaps
with the strongest H$_2$O features. The constraints possible with HRS on the
molecular species can be used for compositional analysis and to study the
chemical diversity of such planets in the future.
