Problem eating pastry up in a layer (7)
I believe the answer is:
stratum
'a layer' is the definition.
(stratum is a kind of layer)
'problem eating pastry up' is the wordplay.
'problem' becomes 'sum' (arithmetic problem).
'eating' means one lot of letters goes inside another.
'pastry' becomes 'tart' (tart is a kind of pastry).
'up' shows that the letters should be reversed in order (in down clue: letters go upwards).
'tart' reversed gives 'trat'.
'sum' placed around 'trat' is 'STRATUM'.
'in' is the link.
(Other definitions for stratum that I've seen before include "stretch of rock" , "Bed of sedimentary rock" , "Social class - level" , "(Geological) layer" , "Layer (of rock)" .)