Rock at the lowest level beginning on top (6)
I believe the answer is:
basalt
'rock' is the definition.
(I know that basalt is a type of volcanic rock)
'the lowest level beginning on top' is the wordplay.
'the lowest level' becomes 'basal' (I've seen this before).
'beginning on' indicates taking the first letters.
The initial letter of 'top' is 't'.
'basal'+'t'='BASALT'
'at' is the link.
(Other definitions for basalt that I've seen before include "Type of rock is a blast, oddly" , "Dark fine-grained volcanic rock" , "Black volcanic rock" , "Rock containing olivine" , "Common volcanic rock" .)