Affixes and lexical verbs in Malay occupy the same head position in the verb phrase (VP). This raises the question of how is it that these two different morphemes with different syntactic categories - one a functional head and the other a lexical head - could occupy the same head position in a verb phrase of a sentence in Malay. This article will attempt to shed some light on this question. In this article, we will analyse the verb phrase structure in Malay using the Minimalist Program Approach. Based on Larson (1988) and Chomsky (1995), we will posit the VP shell hypothesis in which the verb phrase structure in Malay has two layers of the VP: one is the VP and the other is a small v (little verb phrase vP). Based on these two layers of the verb phrase, this discussion will revolve around the notion that each of these two layers has its own head and projections in their own VP structures. The head position of the VP node is occupied by the lexical verb while the affix is based-generated at the head v of the vP, which is a functional category. We will use, as examples, Malay active and passive sentences and demonstrate how this two-layer analysis could adequately describe Malay sentences. We assume that each sentence has its own functional heads which are used to hold affixes: active or passive affixes.