Thin floor machining is a challenging and demanding issue, due to vibrations that create poor surface quality. Several technologies have been developed to overcome this problem. Ad hoc fixtures for a given part geometry lead to meeting quality tolerances, but since they lack flexibility, they are expensive and not suitable for low manufacturing batches. On the contrary, flexible fixtures consisting of vacuum cups adaptable to a diversity of part geometries may not totally avoid vibrations, which greatly limits its use. The present study analyses the feasibility of thin floor milling in terms of vibration and roughness, in the cases where milling is conducted without back support, a usual situation when flexible fixtures are employed, so as to define the conditions for a stable milling in them and thus avoid the use of ad hoc fixtures. For that purpose, the change of modal parameters due to material removal and its influence on chatter appearance have been studied, by means of stability lobe diagrams and Fourier Transform analysis. Additionally, the relationship between surface roughness and chatter frequency, tooth passing frequency, and spindle frequency have been studied. Ploughing effect has also been observed during milling, and the factors that lead to the appearance of this undesirable effect have been analyzed, in order to avoid it. It has been proven that finish milling of thin floors without support in the axial direction of the mill can meet aeronautic tolerances and requirements, providing that proper cutting conditions and machining zones are selected.