I generated a project using MQX and Processor Expert. This is the configuration for System Clocks

And this is the generated code for CMT.c
/* ###################################################################
** THIS COMPONENT MODULE IS GENERATED BY THE TOOL. DO NOT MODIFY IT.
** Filename : CMT.c
** Project : ProcessorExpert
** Processor : MK60DN256VLQ10
** Component : Init_CMT
** Version : Component 01.006, Driver 01.06, CPU db: 3.00.000
** Compiler : GNU C Compiler
** Date/Time : 2013-09-03, 13:39, # CodeGen: 2
** Abstract :
** This file implements the CMT (CMT) module initialization
** according to the Peripheral Initialization settings, and
** defines interrupt service routines prototypes.
** Settings :
** Component name : CMT
** Device : CMT
** Settings :
** Clock gate : Do not initialize
** Clock setting :
** Primary prescaler divider : divide by 1
** Clock divide prescaler : divide by 1
** Input clock freqency : 50 MHz
** Carrier generator :
** Primary carrier high time value : 0
** Primary carrier high time : 0 us
** Primary carrier low time value : 0
** Primary carrier low time : 0 us
** Primary carrier frequency : 0 MHz
** Secondary carrier high time value : 0
** Secondary carrier high time : 0 us
** Secondary carrier low time value : 0
** Secondary carrier low time : 0 us
** Secondary carrier frequency : 0 MHz
** Mode : Time
** Modulator :
** Mark period data : 0
** Mark pulse length : 0.16 us
** Space period data : 0
** Space pulse length : 0 us
** Pins :
** Output pin : PTD7/CMT_IRO/UART0_TX/FTM0_CH7/FTM0_FLT1
** Output pin signal :
** Output pin enabled : no
** Output pin active polarity : Low
** Init output pin latch value : Low
** Interrupts/DMA :
** End of cycle interrupt/DMA :
** Interrupt : INT_CMT
** Interrupt request : Disabled
** Interrupt priority : 0 (Highest)
** ISR Name :
** End of cycle interrupt : Disabled
** Request type : Interrupt
** Initialization :
** Enable modulator and carrier generator : no
** Extended space operation in init : Disabled
** Call Init method : yes
** Contents :
** Init - void CMT_Init(void);
**
** Copyright : 1997 - 2013 Freescale Semiconductor, Inc. All Rights Reserved.
** SOURCE DISTRIBUTION PERMISSIBLE as directed in End User License Agreement.
**
** http : www.freescale.com
** mail : support@freescale.com
** ###################################################################*/
/*!
** @file CMT.c
** @version 01.06
** @brief
** This file implements the CMT (CMT) module initialization
** according to the Peripheral Initialization settings, and
** defines interrupt service routines prototypes.
*/
/*!
** @addtogroup CMT_module CMT module documentation
** @{
*/
/* MODULE CMT. */
#include "CMT.h"
/* Including shared modules, which are used in the whole project */
#include "PE_Types.h"
#include "PE_Error.h"
#include "PE_Const.h"
#include "IO_Map.h"
#include "Cpu.h"
/*
** ===================================================================
** Method : CMT_Init (component Init_CMT)
** Description :
** This method initializes registers of the CMT module
** according to the Peripheral Initialization settings.
** Call this method in user code to initialize the module. By
** default, the method is called by PE automatically; see "Call
** Init method" property of the component for more details.
** Parameters : None
** Returns : Nothing
** ===================================================================
*/
void CMT_Init(void)
{
/* Clear interrupt flags */
(void)(CMT_MSC == 0U);
(void)(CMT_CMD2 == 0U);
/* CMT_OC: IROL=0,CMTPOL=0,IROPEN=0,??=0,??=0,??=0,??=0,??=0 */
CMT_OC = 0x00U;
/* CMT_PPS: ??=0,??=0,??=0,??=0,PPSDIV=0 */
CMT_PPS = CMT_PPS_PPSDIV(0x00);
/* CMT_CGH1: PH=0 */
CMT_CGH1 = CMT_CGH1_PH(0x00);
/* CMT_CGL1: PL=0 */
CMT_CGL1 = CMT_CGL1_PL(0x00);
/* CMT_CGH2: SH=0 */
CMT_CGH2 = CMT_CGH2_SH(0x00);
/* CMT_CGL2: SL=0 */
CMT_CGL2 = CMT_CGL2_SL(0x00);
/* CMT_CMD1: MB=0 */
CMT_CMD1 = CMT_CMD1_MB(0x00);
/* CMT_CMD2: MB=0 */
CMT_CMD2 = CMT_CMD2_MB(0x00);
/* CMT_CMD3: SB=0 */
CMT_CMD3 = CMT_CMD3_SB(0x00);
/* CMT_CMD4: SB=0 */
CMT_CMD4 = CMT_CMD4_SB(0x00);
/* CMT_DMA: ??=0,??=0,??=0,??=0,??=0,??=0,??=0,DMA=0 */
CMT_DMA = 0x00U;
/* CMT_MSC: EOCF=0,CMTDIV=0,EXSPC=0,BASE=0,FSK=0,EOCIE=0,MCGEN=0 */
CMT_MSC = CMT_MSC_CMTDIV(0x00);
}
/* END CMT. */
/*!
** @}
*/
/*
** ###################################################################
**
** This file was created by Processor Expert 10.2 [05.06]
** for the Freescale Kinetis series of microcontrollers.
**
** ###################################################################
*/