$(document).on('click','#submit',function(){
console.log($('#prescricao[qtd][1]').val());
});<script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.1/jquery.min.js"></script><inputtype="text" name="prescricao" id="prescricao[qtd][1]" class="form-control input-md prescricao" autocomplete="off" placeholder="" tabindex="2"/>
<button name="Cadastrar" class="btn btn-success" id="submit">Cadastrar</button> You have to escape [] within the string because it will be interpreted as a CSS selector and in selectors [] means attribute selector in HTML. So with \ before each [] will already give.
$(document).on('click', '#submit', function() {
console.log($('#prescricao\[qtd\]\[1\]').val());
});<script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.1/jquery.min.js"></script><inputtype="text" name="prescricao" id="prescricao[qtd][1]" class="form-control input-md prescricao" autocomplete="off" placeholder="" tabindex="2" />
<button name="Cadastrar" class="btn btn-success" id="submit">Cadastrar</button>