Mart arranged nine in array (6)
I believe the answer is:
matrix
'array' is the definition.
(I know this)
'mart arranged nine' is the wordplay.
'arranged' indicates an anagram.
'nine' becomes 'IX' (roman numeral).
'mart' is an anagram of 'matr'.
'matr'+'ix'='MATRIX'
'in' is the link.
(Other definitions for matrix that I've seen before include "Grid-like pattern of elements" , "Mathematical array of numbers" , "Grid-like array of rat mix" , "Frame - template" , "Rectangular array of quantities or symbols" .)